rs2026628

Variant names:

• chr10-6667696-A-G
• rs2026628

Your query was ambiguous. Multiple possible variants found:

• chr10-6667696-A-G
• chr10-6667696-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 0.534 in 151,974 control chromosomes in the GnomAD database, including 22,138 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 0.53 (22138 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.444
• Publications: 8 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 (EAS) allele frequency at 95% confidence interval = 0.745 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: 0.534 AC: 81130 AN: 151856 Hom.: 22104 Cov.: 31

Gnomad AFR AF: 0.457

Gnomad AMI AF: 0.469

Gnomad AMR AF: 0.634

Gnomad ASJ AF: 0.503

Gnomad EAS AF: 0.764

Gnomad SAS AF: 0.514

Gnomad FIN AF: 0.548

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.543

Gnomad OTH AF: 0.537

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

GnomAD4 genome AF: 0.534 AC: 81206 AN: 151974 Hom.: 22138 Cov.: 31 AF XY: 0.540 AC XY: 40082 AN XY: 74268

African (AFR) AF: 0.457 AC: 18942 AN: 41436

American (AMR) AF: 0.634 AC: 9685 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.503 AC: 1747 AN: 3470

East Asian (EAS) AF: 0.765 AC: 3956 AN: 5172

South Asian (SAS) AF: 0.513 AC: 2472 AN: 4816

European-Finnish (FIN) AF: 0.548 AC: 5784 AN: 10554

Middle Eastern (MID) AF: 0.558 AC: 164 AN: 294

European-Non Finnish (NFE) AF: 0.543 AC: 36882 AN: 67946

Other (OTH) AF: 0.544 AC: 1148 AN: 2112

Alfa AF: 0.539 Hom.: 33097

Bravo AF: 0.541

Asia WGS AF: 0.644 AC: 2237 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	1.0
DANN	Benign	0.53
PhyloP100		-0.44

Splicing

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

Other links and lift over

dbSNP: rs2026628; hg19: chr10-6709658;