chr13-62356167-A-G

Variant names:

• chr13-62356167-A-G
• rs9563960

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 0.244 in 151,988 control chromosomes in the GnomAD database, including 4,894 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 0.24 (4894 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.246
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.31 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: 0.244 AC: 37099 AN: 151870 Hom.: 4891 Cov.: 32

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.273

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.222

Gnomad EAS AF: 0.203

Gnomad SAS AF: 0.263

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.313

Gnomad OTH AF: 0.247

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

GnomAD4 genome AF: 0.244 AC: 37107 AN: 151988 Hom.: 4894 Cov.: 32 AF XY: 0.236 AC XY: 17566 AN XY: 74312

African (AFR) AF: 0.173 AC: 7194 AN: 41482

American (AMR) AF: 0.188 AC: 2876 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.222 AC: 770 AN: 3468

East Asian (EAS) AF: 0.203 AC: 1047 AN: 5168

South Asian (SAS) AF: 0.264 AC: 1273 AN: 4826

European-Finnish (FIN) AF: 0.172 AC: 1815 AN: 10580

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.313 AC: 21280 AN: 67886

Other (OTH) AF: 0.245 AC: 518 AN: 2110

Alfa AF: 0.275 Hom.: 778

Bravo AF: 0.240

Asia WGS AF: 0.225 AC: 780 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.8
DANN	Benign	0.72
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs9563960; hg19: chr13-62930300;