chr2-182831792-T-C

Variant names:

• chr2-182831792-T-C
• rs17265803

Variant summary

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

The variant allele was found at a frequency of 0.0756 in 152,126 control chromosomes in the GnomAD database, including 551 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 0.076 (551 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.51
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.105 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

Frequencies

GnomAD3 genomes AF: 0.0757 AC: 11508 AN: 152008 Hom.: 554 Cov.: 31

Gnomad AFR AF: 0.0257

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.0491

Gnomad ASJ AF: 0.111

Gnomad EAS AF: 0.0363

Gnomad SAS AF: 0.0699

Gnomad FIN AF: 0.121

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.0570

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

GnomAD4 genome AF: 0.0756 AC: 11501 AN: 152126 Hom.: 551 Cov.: 31 AF XY: 0.0757 AC XY: 5631 AN XY: 74358

African (AFR) AF: 0.0256 AC: 1065 AN: 41532

American (AMR) AF: 0.0489 AC: 747 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.111 AC: 387 AN: 3472

East Asian (EAS) AF: 0.0362 AC: 187 AN: 5168

South Asian (SAS) AF: 0.0696 AC: 335 AN: 4816

European-Finnish (FIN) AF: 0.121 AC: 1274 AN: 10564

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.107 AC: 7257 AN: 67992

Other (OTH) AF: 0.0560 AC: 118 AN: 2108

Alfa AF: 0.0929 Hom.: 877

Bravo AF: 0.0678

Asia WGS AF: 0.0430 AC: 150 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.44
DANN	Benign	0.74
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs17265803; hg19: chr2-183696519;