rs375528237

Variant names:

• chrX-101278075-C-A
• rs375528237
• NM_001168474.2:c.551G>T

Your query was ambiguous. Multiple possible variants found:

• chrX-101278075-C-A
• chrX-101278075-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001168474.2(TAF7L):​c.551G>T​(p.Arg184Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R184H) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 23)
• Consequence: TAF7L NM_001168474.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.33

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

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.24297613).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TAF7L	NM_001168474.2	c.551G>T	p.Arg184Leu	missense_variant	Exon 8 of 13	ENST00000356784.2	NP_001161946.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TAF7L	ENST00000356784.2	c.551G>T	p.Arg184Leu	missense_variant	Exon 8 of 13	1	NM_001168474.2	ENSP00000349235.1
TAF7L	ENST00000372907.7	c.809G>T	p.Arg270Leu	missense_variant	Exon 8 of 13	1		ENSP00000361998.3
TAF7L	ENST00000324762.10	c.551G>T	p.Arg184Leu	missense_variant	Exon 7 of 11	2		ENSP00000320283.6

Frequencies

GnomAD3 genomes Cov.: 23

GnomAD3 exomes AF: 0.00000546 AC: 1 AN: 183211 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 67669

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000122

Gnomad OTH exome AF: 0.00

GnomAD4 exome Cov.: 29

GnomAD4 genome Cov.: 23

ExAC AF: 0.00000824 AC: 1

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.14
BayesDel_addAF	Benign	-0.34	T
BayesDel_noAF	Benign	-0.73
CADD	Benign	3.5
DANN	Benign	0.96
DEOGEN2	Benign	0.29	T;.;.
FATHMM_MKL	Uncertain	0.91	D
LIST_S2	Benign	0.84	T;D;D
M_CAP	Uncertain	0.26	D
MetaRNN	Benign	0.24	T;T;T
MetaSVM	Benign	-1.1	T
MutationAssessor	Uncertain	2.2	M;.;.
PrimateAI	Benign	0.20	T
PROVEAN	Benign	-2.0	N;N;N
REVEL	Benign	0.061
Sift	Benign	0.16	T;T;T
Sift4G	Benign	0.19	T;T;T
Polyphen		0.088	B;B;.
Vest4		0.33
MutPred		0.62		Loss of MoRF binding (P = 0.0268);.;.;
MVP		0.093
MPC		0.45
ClinPred		0.12	T
GERP RS		-0.059
Varity_R		0.095
gMVP		0.40

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

Other links and lift over

dbSNP: rs375528237; hg19: chrX-100533063;