13-86540492-C-T

Variant names:

• chr13-86540492-C-T
• rs9301538

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 0.645 in 151,616 control chromosomes in the GnomAD database, including 31,956 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 0.64 (31956 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.536
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.76 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: 0.645 AC: 97643 AN: 151498 Hom.: 31917 Cov.: 32

Gnomad AFR AF: 0.767

Gnomad AMI AF: 0.708

Gnomad AMR AF: 0.636

Gnomad ASJ AF: 0.573

Gnomad EAS AF: 0.509

Gnomad SAS AF: 0.560

Gnomad FIN AF: 0.607

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.598

Gnomad OTH AF: 0.624

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

GnomAD4 genome AF: 0.645 AC: 97740 AN: 151616 Hom.: 31956 Cov.: 32 AF XY: 0.641 AC XY: 47505 AN XY: 74056

African (AFR) AF: 0.767 AC: 31777 AN: 41446

American (AMR) AF: 0.637 AC: 9700 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.573 AC: 1987 AN: 3466

East Asian (EAS) AF: 0.508 AC: 2615 AN: 5148

South Asian (SAS) AF: 0.560 AC: 2696 AN: 4816

European-Finnish (FIN) AF: 0.607 AC: 6373 AN: 10502

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.598 AC: 40448 AN: 67686

Other (OTH) AF: 0.627 AC: 1324 AN: 2110

Alfa AF: 0.608 Hom.: 12966

Bravo AF: 0.653

Asia WGS AF: 0.604 AC: 2098 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.94
DANN	Benign	0.43
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs9301538; hg19: chr13-87192747;