chr10-61589009-G-T

Variant names:

• chr10-61589009-G-T
• rs1350172

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 0.649 in 151,856 control chromosomes in the GnomAD database, including 32,296 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 0.65 (32296 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.34
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.678 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: 0.648 AC: 98387 AN: 151738 Hom.: 32251 Cov.: 32

Gnomad AFR AF: 0.684

Gnomad AMI AF: 0.758

Gnomad AMR AF: 0.654

Gnomad ASJ AF: 0.616

Gnomad EAS AF: 0.382

Gnomad SAS AF: 0.567

Gnomad FIN AF: 0.685

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.646

Gnomad OTH AF: 0.630

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

GnomAD4 genome AF: 0.649 AC: 98487 AN: 151856 Hom.: 32296 Cov.: 32 AF XY: 0.646 AC XY: 47959 AN XY: 74206

African (AFR) AF: 0.685 AC: 28353 AN: 41418

American (AMR) AF: 0.654 AC: 9980 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.616 AC: 2133 AN: 3462

East Asian (EAS) AF: 0.381 AC: 1951 AN: 5116

South Asian (SAS) AF: 0.568 AC: 2730 AN: 4806

European-Finnish (FIN) AF: 0.685 AC: 7245 AN: 10572

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.646 AC: 43906 AN: 67914

Other (OTH) AF: 0.628 AC: 1324 AN: 2108

Alfa AF: 0.657 Hom.: 4790

Bravo AF: 0.647

Asia WGS AF: 0.486 AC: 1692 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	12
DANN	Benign	0.68
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs1350172; hg19: chr10-63348767;