rs287983

Variant names:

• chr2-9837608-A-C
• rs287983

Your query was ambiguous. Multiple possible variants found:

• chr2-9837608-A-C
• chr2-9837608-A-G
• chr2-9837608-A-T

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 0.848 in 152,086 control chromosomes in the GnomAD database, including 55,280 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 0.85 (55280 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.480
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.92 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: 0.848 AC: 128936 AN: 151968 Hom.: 55243 Cov.: 31

Gnomad AFR AF: 0.719

Gnomad AMI AF: 0.805

Gnomad AMR AF: 0.890

Gnomad ASJ AF: 0.830

Gnomad EAS AF: 0.901

Gnomad SAS AF: 0.944

Gnomad FIN AF: 0.911

Gnomad MID AF: 0.806

Gnomad NFE AF: 0.899

Gnomad OTH AF: 0.843

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

GnomAD4 genome AF: 0.848 AC: 129033 AN: 152086 Hom.: 55280 Cov.: 31 AF XY: 0.851 AC XY: 63288 AN XY: 74342

African (AFR) AF: 0.720 AC: 29824 AN: 41450

American (AMR) AF: 0.890 AC: 13605 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.830 AC: 2881 AN: 3472

East Asian (EAS) AF: 0.901 AC: 4655 AN: 5168

South Asian (SAS) AF: 0.943 AC: 4548 AN: 4822

European-Finnish (FIN) AF: 0.911 AC: 9644 AN: 10588

Middle Eastern (MID) AF: 0.795 AC: 232 AN: 292

European-Non Finnish (NFE) AF: 0.899 AC: 61125 AN: 67988

Other (OTH) AF: 0.846 AC: 1785 AN: 2110

Alfa AF: 0.871 Hom.: 9493

Bravo AF: 0.838

Asia WGS AF: 0.919 AC: 3197 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
DANN	Benign	0.64
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs287983; hg19: chr2-9977737;