rs2479967

Variant names:

• chr13-111319384-G-A
• rs2479967
• NM_001303133.1:c.-110-1473G>A

Your query was ambiguous. Multiple possible variants found:

• chr13-111319384-G-A
• chr13-111319384-G-C
• chr13-111319384-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001303133.1(TEX29):​c.-110-1473G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.28 in 152,058 control chromosomes in the GnomAD database, including 6,853 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.28 (6853 hom., cov: 32)
• Consequence: TEX29 NM_001303133.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.613
• Publications: 6 publications found

Genes affected

TEX29 (HGNC:20370): (testis expressed 29) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

LOC105370365 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.795 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TEX29	NM_001303133.1	c.-110-1473G>A		intron_variant	Intron 1 of 6		NP_001290062.1
TEX29	XM_017020387.2	c.48-1473G>A		intron_variant	Intron 1 of 5		XP_016875876.2
LOC105370365	XR_001750031.3	n.118-170C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TEX29	ENST00000497241.5	n.48-1473G>A		intron_variant	Intron 1 of 6	5		ENSP00000431661.1

Frequencies

GnomAD3 genomes AF: 0.279 AC: 42465 AN: 151940 Hom.: 6845 Cov.: 32

Gnomad AFR AF: 0.253

Gnomad AMI AF: 0.219

Gnomad AMR AF: 0.359

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.816

Gnomad SAS AF: 0.346

Gnomad FIN AF: 0.282

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.267

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.280 AC: 42502 AN: 152058 Hom.: 6853 Cov.: 32 AF XY: 0.287 AC XY: 21353 AN XY: 74342

African (AFR) AF: 0.253 AC: 10490 AN: 41464

American (AMR) AF: 0.360 AC: 5502 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.163 AC: 566 AN: 3468

East Asian (EAS) AF: 0.816 AC: 4215 AN: 5166

South Asian (SAS) AF: 0.347 AC: 1667 AN: 4810

European-Finnish (FIN) AF: 0.282 AC: 2983 AN: 10582

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.239 AC: 16247 AN: 67970

Other (OTH) AF: 0.273 AC: 576 AN: 2108

Alfa AF: 0.272 Hom.: 1173

Bravo AF: 0.289

Asia WGS AF: 0.559 AC: 1942 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.5
DANN	Benign	0.71
PhyloP100		0.61

Splicing

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

Other links and lift over

dbSNP: rs2479967; hg19: chr13-111971731;