rs2026628

Positions:

• chr10-6667696-A-G
• chr10-6667696-A-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.457

Gnomad4 AMR AF: 0.634

Gnomad4 ASJ AF: 0.503

Gnomad4 EAS AF: 0.765

Gnomad4 SAS AF: 0.513

Gnomad4 FIN AF: 0.548

Gnomad4 NFE AF: 0.543

Gnomad4 OTH AF: 0.544

Alfa AF: 0.539 Hom.: 27846

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2026628; hg19: chr10-6709658;