3-51702628-T-C

Variant names:

• chr3-51702628-T-C
• rs3821829
• NM_015926.6:c.650-1096T>C

Variant summary

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

The NM_015926.6(TEX264):​c.650-1096T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.884 in 152,264 control chromosomes in the GnomAD database, including 59,662 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 0.88 (59662 hom., cov: 34)
• Consequence: TEX264 NM_015926.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.380
• Publications: 7 publications found

Genes affected

TEX264 (HGNC:30247): (testis expressed 264, ER-phagy receptor) Enables signaling receptor activity. Involved in protein-DNA covalent cross-linking repair. Acts upstream of or within reticulophagy. Located in several cellular components, including autophagosome membrane; endoplasmic reticulum membrane; and replication fork. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000298202 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.929 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TEX264	NM_015926.6	c.650-1096T>C		intron_variant	Intron 4 of 4	ENST00000341333.10	NP_057010.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TEX264	ENST00000341333.10	c.650-1096T>C		intron_variant	Intron 4 of 4	1	NM_015926.6	ENSP00000340969.5

Frequencies

GnomAD3 genomes AF: 0.884 AC: 134477 AN: 152146 Hom.: 59603 Cov.: 34

Gnomad AFR AF: 0.936

Gnomad AMI AF: 0.838

Gnomad AMR AF: 0.870

Gnomad ASJ AF: 0.873

Gnomad EAS AF: 0.940

Gnomad SAS AF: 0.877

Gnomad FIN AF: 0.870

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.855

Gnomad OTH AF: 0.883

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

GnomAD4 genome AF: 0.884 AC: 134594 AN: 152264 Hom.: 59662 Cov.: 34 AF XY: 0.885 AC XY: 65896 AN XY: 74446

African (AFR) AF: 0.937 AC: 38923 AN: 41562

American (AMR) AF: 0.870 AC: 13319 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.873 AC: 3032 AN: 3472

East Asian (EAS) AF: 0.940 AC: 4869 AN: 5178

South Asian (SAS) AF: 0.876 AC: 4227 AN: 4824

European-Finnish (FIN) AF: 0.870 AC: 9233 AN: 10610

Middle Eastern (MID) AF: 0.878 AC: 258 AN: 294

European-Non Finnish (NFE) AF: 0.855 AC: 58101 AN: 67994

Other (OTH) AF: 0.884 AC: 1869 AN: 2114

Alfa AF: 0.865 Hom.: 7100

Bravo AF: 0.887

Asia WGS AF: 0.909 AC: 3160 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	7.0
DANN	Benign	0.43
PhyloP100		-0.38
Mutation Taster		=100/0	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: rs3821829; hg19: chr3-51736644;