Genetic Variant ENST00000372907.7:c.101T>C (chrX-101292945-A-G) – ACMG Classification: Likely_benign (-5 pts)

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_StrongBP6

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. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in Lovd as Benign (no stars). Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.

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

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:

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -5 ACMG points.

BP4

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

BP6

Variant X-101292945-A-G is Benign according to our data. Variant chrX-101292945-A-G is described in Lovd as [Benign].

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	Q5H9L4-1
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		Q5H9L4-1

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

107526

AN:

108494

Hom.:

38182

Cov.:

AF XY:

0.992

AC XY:

30473

AN XY:

30732

FAILED QC

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

GnomAD3 exomes

AF:

0.991

AC:

181518

AN:

183187

Hom.:

56665

AF XY:

0.991

AC XY:

67158

AN XY:

67773

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 SAS exome

AF:

0.994

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

Gnomad4 AFR exome

AF:

0.999

Gnomad4 AMR exome

AF:

0.997

Gnomad4 ASJ exome

AF:

0.996

Gnomad4 EAS exome

AF:

1.00

Gnomad4 SAS exome

AF:

0.994

Gnomad4 FIN exome

AF:

0.984

Gnomad4 NFE exome

AF:

0.983

Gnomad4 OTH exome

AF:

0.988

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

Gnomad4 AFR

AF:

0.998

Gnomad4 AMR

AF:

0.997

Gnomad4 ASJ

AF:

0.998

Gnomad4 EAS

AF:

1.00

Gnomad4 SAS

AF:

0.993

Gnomad4 FIN

AF:

0.986

Gnomad4 NFE

AF:

0.986

Gnomad4 OTH

AF:

0.995

Alfa

AF:

0.987

Hom.:

93015

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

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

PrimateAI

Benign

0.21

PROVEAN

Benign

1.8

REVEL

Benign

0.034

Sift

Benign

0.91

Sift4G

Benign

0.31

Polyphen

0.0

Vest4

0.0080

MPC

0.43

ClinPred

0.0021

GERP RS

-2.8

Varity_R

0.045

gMVP

0.093

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over