rs2479967

Positions:

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

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001750031.3(LOC105370365):​n.118-170C>T variant causes a intron, non coding transcript 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: LOC105370365 XR_001750031.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.613

Genes affected

LOC105370365 (HGNC:):

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LOC105370365	XR_001750031.3	n.118-170C>T		intron_variant, non_coding_transcript_variant
TEX29	NM_001303133.1	c.-110-1473G>A		intron_variant			NP_001290062.1
TEX29	XM_017020387.2	c.48-1473G>A		intron_variant			XP_016875876.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TEX29	ENST00000497241.5	c.48-1473G>A		intron_variant, NMD_transcript_variant		5		ENSP00000431661

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

Gnomad4 AFR AF: 0.253

Gnomad4 AMR AF: 0.360

Gnomad4 ASJ AF: 0.163

Gnomad4 EAS AF: 0.816

Gnomad4 SAS AF: 0.347

Gnomad4 FIN AF: 0.282

Gnomad4 NFE AF: 0.239

Gnomad4 OTH AF: 0.273

Alfa AF: 0.273 Hom.: 1148

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2479967; hg19: chr13-111971731;