chr13-62820660-T-C

Variant names:

• chr13-62820660-T-C
• rs1335688

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 0.18 in 151,558 control chromosomes in the GnomAD database, including 4,461 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 0.18 (4461 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.200
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.793 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: 0.180 AC: 27330 AN: 151440 Hom.: 4455 Cov.: 31

Gnomad AFR AF: 0.0375

Gnomad AMI AF: 0.0846

Gnomad AMR AF: 0.315

Gnomad ASJ AF: 0.146

Gnomad EAS AF: 0.814

Gnomad SAS AF: 0.268

Gnomad FIN AF: 0.349

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.200

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

GnomAD4 genome AF: 0.180 AC: 27349 AN: 151558 Hom.: 4461 Cov.: 31 AF XY: 0.196 AC XY: 14486 AN XY: 74046

African (AFR) AF: 0.0375 AC: 1555 AN: 41480

American (AMR) AF: 0.316 AC: 4788 AN: 15152

Ashkenazi Jewish (ASJ) AF: 0.146 AC: 505 AN: 3452

East Asian (EAS) AF: 0.814 AC: 4141 AN: 5090

South Asian (SAS) AF: 0.269 AC: 1296 AN: 4822

European-Finnish (FIN) AF: 0.349 AC: 3686 AN: 10552

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.160 AC: 10819 AN: 67706

Other (OTH) AF: 0.204 AC: 429 AN: 2100

Alfa AF: 0.165 Hom.: 331

Bravo AF: 0.179

Asia WGS AF: 0.465 AC: 1612 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.4
DANN	Benign	0.62
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs1335688; hg19: chr13-63394793;