chrX-101292945-A-G

Variant names:

• chrX-101292945-A-G
• rs5951328
• ENST00000372907.7:c.101T>C

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28
• Publications: 22 publications found

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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (MetaRNN=1.402261E-6).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000372907.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TAF7L	NM_024885.4		c.101T>C	p.Leu34Pro	missense	Exon 1 of 13	NP_079161.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TAF7L	ENST00000372907.7	TSL:1	c.101T>C	p.Leu34Pro	missense	Exon 1 of 13	ENSP00000361998.3

Frequencies

GnomAD3 genomes AF: 0.991 AC: 107526 AN: 108494 Hom.: 38182 Cov.: 21

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

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.: 59 AF XY: 0.986 AC XY: 358515 AN XY: 363570

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.991 AC: 107583 AN: 108550 Hom.: 38178 Cov.: 21 AF XY: 0.992 AC XY: 30539 AN XY: 30798

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

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 v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.049
BayesDel_addAF	Benign	-1.0	T
BayesDel_noAF	Benign	-1.2
CADD	Benign	0.12
DANN	Benign	0.37
DEOGEN2	Benign	0.019	T
FATHMM_MKL	Benign	0.0014	N
LIST_S2	Benign	0.16	T
MetaRNN	Benign	0.0000014	T
MetaSVM	Benign	-0.97	T
MutationAssessor	Benign	-0.34	N
PhyloP100		-1.3
PrimateAI	Benign	0.21	T
PROVEAN	Benign	1.8	N
REVEL	Benign	0.034
Sift	Benign	0.91	T
Sift4G	Benign	0.31	T
Polyphen		0.0	B
Vest4		0.0080
MPC		0.43
ClinPred		0.0021	T
GERP RS		-2.8
PromoterAI		0.044	Neutral
Varity_R		0.045
gMVP		0.093
Mutation Taster		=300/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs5951328; hg19: chrX-100547933; COSMIC: COSV107441621; COSMIC: COSV107441621;