rs2486954

Variant names:

• chr1-203210278-A-G
• rs2486954

Your query was ambiguous. Multiple possible variants found:

• chr1-203210278-A-G
• chr1-203210278-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 0.188 in 152,192 control chromosomes in the GnomAD database, including 3,632 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 0.19 (3632 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0570
• Publications: 4 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 = 0.559 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: 0.188 AC: 28600 AN: 152074 Hom.: 3621 Cov.: 32

Gnomad AFR AF: 0.0583

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.262

Gnomad ASJ AF: 0.220

Gnomad EAS AF: 0.575

Gnomad SAS AF: 0.442

Gnomad FIN AF: 0.184

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.214

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

GnomAD4 genome AF: 0.188 AC: 28629 AN: 152192 Hom.: 3632 Cov.: 32 AF XY: 0.196 AC XY: 14617 AN XY: 74402

African (AFR) AF: 0.0584 AC: 2427 AN: 41546

American (AMR) AF: 0.263 AC: 4023 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.220 AC: 765 AN: 3470

East Asian (EAS) AF: 0.576 AC: 2979 AN: 5174

South Asian (SAS) AF: 0.442 AC: 2134 AN: 4826

European-Finnish (FIN) AF: 0.184 AC: 1950 AN: 10582

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.202 AC: 13702 AN: 67998

Other (OTH) AF: 0.214 AC: 451 AN: 2110

Alfa AF: 0.0914 Hom.: 122

Bravo AF: 0.184

Asia WGS AF: 0.461 AC: 1602 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	2.1
DANN	Benign	0.70
PhyloP100		-0.057

Splicing

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

Other links and lift over

dbSNP: rs2486954; hg19: chr1-203179406;