Genetic Variant ENST00000372907.7:c.101T>C (chrX-101292945-A-G) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000372907.7(TAF7L):c.101T>C(p.Leu34Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.99 ( 38178 hom., 30539 hem., cov: 21)

Exomes 𝑓: 0.99 ( 356626 hom. 358515 hem. )

Failed GnomAD Quality Control

Consequence

TAF7L
ENST00000372907.7 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.28

Publications

22 publications found

Variant links:

Genes affected

TAF7L (HGNC:11548): (TATA-box binding protein associated factor 7 like) This gene is similar to a mouse gene that encodes a TATA box binding protein-associated factor, and shows testis-specific expression. The encoded protein could be a spermatogenesis-specific component of the DNA-binding general transcription factor complex TFIID. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2009]

TAF7L links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=1.402261E-6).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TAF7L	NM_024885.4 link	c.101T>C	p.Leu34Pro	missense_variant	Exon 1 of 13		NP_079161.3
TAF7L	XM_006724664.2 link	c.101T>C	p.Leu34Pro	missense_variant	Exon 1 of 13		XP_006724727.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TAF7L	ENST00000372907.7 link	c.101T>C	p.Leu34Pro	missense_variant	Exon 1 of 13	1		ENSP00000361998.3

Frequencies

GnomAD3 genomes

AF:

0.991

AC:

107526

AN:

108494

Hom.:

38182

Cov.:

show subpopulations

Gnomad AFR

AF:

0.998

Gnomad AMI

AF:

1.00

Gnomad AMR

AF:

0.997

Gnomad ASJ

AF:

0.998

Gnomad EAS

AF:

1.00

Gnomad SAS

AF:

0.993

Gnomad FIN

AF:

0.986

Gnomad MID

AF:

0.987

Gnomad NFE

AF:

0.986

Gnomad OTH

AF:

0.994

GnomAD2 exomes

AF:

0.991

AC:

181518

AN:

183187

AF XY:

0.991

show subpopulations

Gnomad AFR exome

AF:

0.998

Gnomad AMR exome

AF:

0.997

Gnomad ASJ exome

AF:

0.997

Gnomad EAS exome

AF:

1.00

Gnomad FIN exome

AF:

0.985

Gnomad NFE exome

AF:

0.986

Gnomad OTH exome

AF:

0.989

GnomAD4 exome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.986

AC:

1082358

AN:

1098208

Hom.:

356626

Cov.:

AF XY:

0.986

AC XY:

358515

AN XY:

363570

show subpopulations

African (AFR)

AF:

0.999

AC:

26368

AN:

26402

American (AMR)

AF:

0.997

AC:

35101

AN:

35207

Ashkenazi Jewish (ASJ)

AF:

0.996

AC:

19314

AN:

19386

East Asian (EAS)

AF:

1.00

AC:

30205

AN:

30206

South Asian (SAS)

AF:

0.994

AC:

53838

AN:

54149

European-Finnish (FIN)

AF:

0.984

AC:

39846

AN:

40485

Middle Eastern (MID)

AF:

0.996

AC:

4119

AN:

4136

European-Non Finnish (NFE)

AF:

0.983

AC:

828008

AN:

842139

Other (OTH)

AF:

0.988

AC:

45559

AN:

46098

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.477

Heterozygous variant carriers

680

1360

2040

2720

3400

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

21500

43000

64500

86000

107500

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.991

AC:

107583

AN:

108550

Hom.:

38178

Cov.:

AF XY:

0.992

AC XY:

30539

AN XY:

30798

show subpopulations

African (AFR)

AF:

0.998

AC:

29659

AN:

29731

American (AMR)

AF:

0.997

AC:

10027

AN:

10059

Ashkenazi Jewish (ASJ)

AF:

0.998

AC:

2619

AN:

2625

East Asian (EAS)

AF:

1.00

AC:

3418

AN:

3418

South Asian (SAS)

AF:

0.993

AC:

2389

AN:

2405

European-Finnish (FIN)

AF:

0.986

AC:

5432

AN:

5508

Middle Eastern (MID)

AF:

0.991

AC:

214

AN:

216

European-Non Finnish (NFE)

AF:

0.986

AC:

51696

AN:

52451

Other (OTH)

AF:

0.995

AC:

1456

AN:

1464

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.510

Heterozygous variant carriers

109

146

182

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

816

1632

2448

3264

4080

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.988

Hom.:

100310

Bravo

AF:

0.993

TwinsUK

AF:

0.987

AC:

3660

ALSPAC

AF:

0.979

AC:

2829

ESP6500AA

AF:

0.997

AC:

3824

ESP6500EA

AF:

0.989

AC:

6651

ExAC

AF:

0.990

AC:

120231

EpiCase

AF:

0.990

EpiControl

AF:

0.987

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.049

BayesDel_addAF

Benign

-1.0

BayesDel_noAF

Benign

-1.2

CADD

Benign

0.12

(source)

DANN

Benign

0.37

DEOGEN2

Benign

0.019

FATHMM_MKL

Benign

0.0014

LIST_S2

Benign

0.16

MetaRNN

Benign

0.0000014

MetaSVM

Benign

-0.97

MutationAssessor

Benign

-0.34

PhyloP100

-1.3

PrimateAI

Benign

0.21

PROVEAN

Benign

1.8

REVEL

Benign

0.034

Sift

Benign

0.91

Sift4G

Benign

0.31

Vest4

0.0080

ClinPred

0.0021

GERP RS

-2.8

PromoterAI

0.044

Neutral

(source)

Varity_R

0.045

gMVP

0.093

Mutation Taster

=300/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over