rs1882347

Variant names:

• chr2-163551804-A-C
• rs1882347

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 0.0761 in 152,202 control chromosomes in the GnomAD database, including 524 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 (524 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.787
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.217 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: 0.0759 AC: 11548 AN: 152084 Hom.: 521 Cov.: 32

Gnomad AFR AF: 0.0749

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.0610

Gnomad ASJ AF: 0.0533

Gnomad EAS AF: 0.228

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.0932

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0646

Gnomad OTH AF: 0.0793

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

GnomAD4 genome AF: 0.0761 AC: 11575 AN: 152202 Hom.: 524 Cov.: 32 AF XY: 0.0790 AC XY: 5880 AN XY: 74406

African (AFR) AF: 0.0753 AC: 3130 AN: 41540

American (AMR) AF: 0.0609 AC: 931 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0533 AC: 185 AN: 3470

East Asian (EAS) AF: 0.228 AC: 1174 AN: 5158

South Asian (SAS) AF: 0.101 AC: 485 AN: 4822

European-Finnish (FIN) AF: 0.0932 AC: 988 AN: 10604

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0646 AC: 4391 AN: 67998

Other (OTH) AF: 0.0828 AC: 175 AN: 2114

Alfa AF: 0.0671 Hom.: 569

Bravo AF: 0.0742

Asia WGS AF: 0.165 AC: 571 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.17
DANN	Benign	0.48
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs1882347; hg19: chr2-164408314;