rs10497473

Variant names:

• chr2-176903861-C-T
• rs10497473
• ENST00000795314.1:n.323+11474C>T

Variant summary

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

The ENST00000795314.1(ENSG00000303534):​n.323+11474C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0625 in 152,220 control chromosomes in the GnomAD database, including 605 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 0.063 (605 hom., cov: 32)
• Consequence: ENSG00000303534 ENST00000795314.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.297
• Publications: 1 publications found

Genes affected

ENSG00000303534 (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 (AFR) allele frequency at 95% confidence interval = 0.164 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000303534	ENST00000795314.1	n.323+11474C>T		intron_variant	Intron 1 of 3
ENSG00000303534	ENST00000795315.1	n.100+11474C>T		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.0624 AC: 9492 AN: 152102 Hom.: 602 Cov.: 32

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0355

Gnomad ASJ AF: 0.0404

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.00807

Gnomad FIN AF: 0.0265

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0207

Gnomad OTH AF: 0.0640

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

GnomAD4 genome AF: 0.0625 AC: 9518 AN: 152220 Hom.: 605 Cov.: 32 AF XY: 0.0605 AC XY: 4505 AN XY: 74416

African (AFR) AF: 0.167 AC: 6950 AN: 41518

American (AMR) AF: 0.0354 AC: 542 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0404 AC: 140 AN: 3466

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5184

South Asian (SAS) AF: 0.00808 AC: 39 AN: 4828

European-Finnish (FIN) AF: 0.0265 AC: 281 AN: 10598

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0207 AC: 1410 AN: 68014

Other (OTH) AF: 0.0662 AC: 140 AN: 2116

Alfa AF: 0.0511 Hom.: 78

Bravo AF: 0.0691

Asia WGS AF: 0.0200 AC: 72 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	12
DANN	Benign	0.50
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs10497473; hg19: chr2-177768589;