rs10208273

Variant names:

• chr2-6383862-A-G
• rs10208273

Your query was ambiguous. Multiple possible variants found:

• chr2-6383862-A-G
• chr2-6383862-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 0.304 in 152,126 control chromosomes in the GnomAD database, including 7,617 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 0.30 (7617 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.217
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.558 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: 0.304 AC: 46193 AN: 152008 Hom.: 7614 Cov.: 33

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.383

Gnomad ASJ AF: 0.410

Gnomad EAS AF: 0.576

Gnomad SAS AF: 0.385

Gnomad FIN AF: 0.291

Gnomad MID AF: 0.346

Gnomad NFE AF: 0.301

Gnomad OTH AF: 0.326

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

GnomAD4 genome AF: 0.304 AC: 46219 AN: 152126 Hom.: 7617 Cov.: 33 AF XY: 0.310 AC XY: 23032 AN XY: 74374

African (AFR) AF: 0.229 AC: 9512 AN: 41506

American (AMR) AF: 0.384 AC: 5877 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.410 AC: 1423 AN: 3472

East Asian (EAS) AF: 0.575 AC: 2978 AN: 5176

South Asian (SAS) AF: 0.387 AC: 1861 AN: 4814

European-Finnish (FIN) AF: 0.291 AC: 3071 AN: 10566

Middle Eastern (MID) AF: 0.348 AC: 101 AN: 290

European-Non Finnish (NFE) AF: 0.301 AC: 20452 AN: 67984

Other (OTH) AF: 0.325 AC: 685 AN: 2110

Alfa AF: 0.308 Hom.: 31594

Bravo AF: 0.310

Asia WGS AF: 0.424 AC: 1470 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.0
DANN	Benign	0.50
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs10208273; hg19: chr2-6523994;