chr10-61602229-C-T

Variant names:

• chr10-61602229-C-T
• rs2814021

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 0.778 in 151,766 control chromosomes in the GnomAD database, including 46,296 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 0.78 (46296 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.832 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.777 AC: 117889 AN: 151648 Hom.: 46224 Cov.: 31

Gnomad AFR AF: 0.839

Gnomad AMI AF: 0.833

Gnomad AMR AF: 0.789

Gnomad ASJ AF: 0.804

Gnomad EAS AF: 0.550

Gnomad SAS AF: 0.583

Gnomad FIN AF: 0.831

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.758

Gnomad OTH AF: 0.773

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

GnomAD4 genome AF: 0.778 AC: 118024 AN: 151766 Hom.: 46296 Cov.: 31 AF XY: 0.777 AC XY: 57612 AN XY: 74164

African (AFR) AF: 0.839 AC: 34780 AN: 41434

American (AMR) AF: 0.789 AC: 12006 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.804 AC: 2788 AN: 3468

East Asian (EAS) AF: 0.550 AC: 2835 AN: 5156

South Asian (SAS) AF: 0.585 AC: 2815 AN: 4816

European-Finnish (FIN) AF: 0.831 AC: 8778 AN: 10564

Middle Eastern (MID) AF: 0.847 AC: 249 AN: 294

European-Non Finnish (NFE) AF: 0.758 AC: 51388 AN: 67810

Other (OTH) AF: 0.775 AC: 1625 AN: 2098

Alfa AF: 0.763 Hom.: 186876

Bravo AF: 0.782

Asia WGS AF: 0.601 AC: 2089 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.12
DANN	Benign	0.40
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs2814021; hg19: chr10-63361987;