13-62832095-A-G

Variant names:

• chr13-62832095-A-G
• rs10507688

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 0.158 in 152,196 control chromosomes in the GnomAD database, including 3,840 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 0.16 (3840 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00500
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.825 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.158 AC: 24030 AN: 152078 Hom.: 3829 Cov.: 32

Gnomad AFR AF: 0.0330

Gnomad AMI AF: 0.0461

Gnomad AMR AF: 0.273

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.846

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.302

Gnomad MID AF: 0.185

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.180

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

GnomAD4 genome AF: 0.158 AC: 24052 AN: 152196 Hom.: 3840 Cov.: 32 AF XY: 0.172 AC XY: 12821 AN XY: 74406

African (AFR) AF: 0.0329 AC: 1368 AN: 41574

American (AMR) AF: 0.275 AC: 4192 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.114 AC: 397 AN: 3470

East Asian (EAS) AF: 0.846 AC: 4362 AN: 5154

South Asian (SAS) AF: 0.193 AC: 931 AN: 4822

European-Finnish (FIN) AF: 0.302 AC: 3195 AN: 10588

Middle Eastern (MID) AF: 0.182 AC: 53 AN: 292

European-Non Finnish (NFE) AF: 0.134 AC: 9121 AN: 68002

Other (OTH) AF: 0.185 AC: 391 AN: 2114

Alfa AF: 0.144 Hom.: 6523

Bravo AF: 0.157

Asia WGS AF: 0.446 AC: 1550 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.6
DANN	Benign	0.52
PhyloP100		0.0050

Splicing

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

Other links and lift over

dbSNP: rs10507688; hg19: chr13-63406228;