rs3006496

Variant names:

• chr10-30270485-C-T
• rs3006496

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 0.563 in 152,102 control chromosomes in the GnomAD database, including 28,137 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 0.56 (28137 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.07
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.734 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.564 AC: 85687 AN: 151982 Hom.: 28139 Cov.: 33

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.717

Gnomad AMR AF: 0.631

Gnomad ASJ AF: 0.610

Gnomad EAS AF: 0.245

Gnomad SAS AF: 0.580

Gnomad FIN AF: 0.769

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.740

Gnomad OTH AF: 0.591

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

GnomAD4 genome AF: 0.563 AC: 85680 AN: 152102 Hom.: 28137 Cov.: 33 AF XY: 0.566 AC XY: 42076 AN XY: 74346

African (AFR) AF: 0.226 AC: 9359 AN: 41460

American (AMR) AF: 0.630 AC: 9635 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.610 AC: 2115 AN: 3470

East Asian (EAS) AF: 0.245 AC: 1271 AN: 5184

South Asian (SAS) AF: 0.580 AC: 2794 AN: 4814

European-Finnish (FIN) AF: 0.769 AC: 8129 AN: 10570

Middle Eastern (MID) AF: 0.660 AC: 194 AN: 294

European-Non Finnish (NFE) AF: 0.740 AC: 50296 AN: 68006

Other (OTH) AF: 0.585 AC: 1233 AN: 2106

Alfa AF: 0.677 Hom.: 154741

Bravo AF: 0.536

Asia WGS AF: 0.404 AC: 1407 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.23
DANN	Benign	0.89
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs3006496; hg19: chr10-30559414;