13-62985342-T-C

Variant names:

• chr13-62985342-T-C
• rs975423

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 0.488 in 151,932 control chromosomes in the GnomAD database, including 19,654 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 0.49 (19654 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.858 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.488 AC: 74087 AN: 151814 Hom.: 19591 Cov.: 31

Gnomad AFR AF: 0.649

Gnomad AMI AF: 0.479

Gnomad AMR AF: 0.481

Gnomad ASJ AF: 0.424

Gnomad EAS AF: 0.879

Gnomad SAS AF: 0.532

Gnomad FIN AF: 0.461

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.367

Gnomad OTH AF: 0.477

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

GnomAD4 genome AF: 0.488 AC: 74211 AN: 151932 Hom.: 19654 Cov.: 31 AF XY: 0.496 AC XY: 36835 AN XY: 74264

African (AFR) AF: 0.650 AC: 26928 AN: 41444

American (AMR) AF: 0.482 AC: 7354 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.424 AC: 1469 AN: 3466

East Asian (EAS) AF: 0.879 AC: 4526 AN: 5148

South Asian (SAS) AF: 0.532 AC: 2561 AN: 4816

European-Finnish (FIN) AF: 0.461 AC: 4864 AN: 10554

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.367 AC: 24929 AN: 67938

Other (OTH) AF: 0.484 AC: 1020 AN: 2108

Alfa AF: 0.400 Hom.: 6632

Bravo AF: 0.497

Asia WGS AF: 0.719 AC: 2497 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.57
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs975423; hg19: chr13-63559475;