rs10495514

Variant names:

• chr2-3169079-G-A
• rs10495514
• ENST00000796916.1:n.267-11951C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000796916.1(ENSG00000303747):​n.267-11951C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0238 in 152,300 control chromosomes in the GnomAD database, including 84 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 0.024 (84 hom., cov: 34)
• Consequence: ENSG00000303747 ENST00000796916.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.492
• Publications: 2 publications found

Genes affected

ENSG00000303747 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BS1: Variant frequency is greater than expected in population eas. GnomAd4 allele frequency = 0.0238 (3622/152300) while in subpopulation EAS AF = 0.0498 (258/5182). AF 95% confidence interval is 0.0448. There are 84 homozygotes in GnomAd4. There are 2003 alleles in the male GnomAd4 subpopulation. Median coverage is 34. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 84 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107985840	XR_001739257.1	n.1121+16944C>T		intron_variant	Intron 2 of 3
LOC107985840	XR_001739258.2	n.1122-11951C>T		intron_variant	Intron 2 of 2
LOC107985840	XR_007086194.1	n.1121+16944C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000303747	ENST00000796916.1	n.267-11951C>T		intron_variant	Intron 2 of 2
ENSG00000303747	ENST00000796917.1	n.152-11951C>T		intron_variant	Intron 1 of 1
ENSG00000303747	ENST00000796918.1	n.153+2378C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0238 AC: 3622 AN: 152182 Hom.: 84 Cov.: 34

Gnomad AFR AF: 0.0176

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0197

Gnomad ASJ AF: 0.0251

Gnomad EAS AF: 0.0499

Gnomad SAS AF: 0.0381

Gnomad FIN AF: 0.0857

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0164

Gnomad OTH AF: 0.0162

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

GnomAD4 genome AF: 0.0238 AC: 3622 AN: 152300 Hom.: 84 Cov.: 34 AF XY: 0.0269 AC XY: 2003 AN XY: 74462

African (AFR) AF: 0.0176 AC: 733 AN: 41560

American (AMR) AF: 0.0196 AC: 300 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0251 AC: 87 AN: 3472

East Asian (EAS) AF: 0.0498 AC: 258 AN: 5182

South Asian (SAS) AF: 0.0380 AC: 183 AN: 4820

European-Finnish (FIN) AF: 0.0857 AC: 909 AN: 10606

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.0164 AC: 1116 AN: 68034

Other (OTH) AF: 0.0161 AC: 34 AN: 2116

Alfa AF: 0.0224 Hom.: 8

Bravo AF: 0.0187

Asia WGS AF: 0.0500 AC: 174 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.2
DANN	Benign	0.63
PhyloP100		0.49

Splicing

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

Other links and lift over

dbSNP: rs10495514; hg19: chr2-3172850;