10-61359108-G-A

Variant names:

• chr10-61359108-G-A
• rs1915447

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 0.387 in 151,850 control chromosomes in the GnomAD database, including 12,264 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 0.39 (12264 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.104
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.473 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: 0.387 AC: 58784 AN: 151732 Hom.: 12254 Cov.: 32

Gnomad AFR AF: 0.271

Gnomad AMI AF: 0.541

Gnomad AMR AF: 0.346

Gnomad ASJ AF: 0.481

Gnomad EAS AF: 0.0930

Gnomad SAS AF: 0.314

Gnomad FIN AF: 0.455

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.477

Gnomad OTH AF: 0.414

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

GnomAD4 genome AF: 0.387 AC: 58807 AN: 151850 Hom.: 12264 Cov.: 32 AF XY: 0.381 AC XY: 28256 AN XY: 74178

African (AFR) AF: 0.271 AC: 11213 AN: 41396

American (AMR) AF: 0.345 AC: 5266 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.481 AC: 1670 AN: 3470

East Asian (EAS) AF: 0.0928 AC: 479 AN: 5160

South Asian (SAS) AF: 0.315 AC: 1516 AN: 4816

European-Finnish (FIN) AF: 0.455 AC: 4789 AN: 10526

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.477 AC: 32407 AN: 67936

Other (OTH) AF: 0.410 AC: 864 AN: 2108

Alfa AF: 0.429 Hom.: 7273

Bravo AF: 0.373

Asia WGS AF: 0.221 AC: 774 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.9
DANN	Benign	0.25
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs1915447; hg19: chr10-63118866;