13-108166537-T-C

Variant names:

• chr13-108166537-T-C
• rs8002852

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 0.0975 in 152,200 control chromosomes in the GnomAD database, including 900 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 0.098 (900 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0550
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.172 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: 0.0977 AC: 14852 AN: 152082 Hom.: 902 Cov.: 32

Gnomad AFR AF: 0.0452

Gnomad AMI AF: 0.108

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.0914

Gnomad EAS AF: 0.182

Gnomad SAS AF: 0.0785

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.0906

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

GnomAD4 genome AF: 0.0975 AC: 14845 AN: 152200 Hom.: 900 Cov.: 32 AF XY: 0.0956 AC XY: 7114 AN XY: 74422

African (AFR) AF: 0.0451 AC: 1872 AN: 41534

American (AMR) AF: 0.103 AC: 1581 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0914 AC: 317 AN: 3470

East Asian (EAS) AF: 0.182 AC: 938 AN: 5160

South Asian (SAS) AF: 0.0792 AC: 382 AN: 4822

European-Finnish (FIN) AF: 0.104 AC: 1107 AN: 10612

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.123 AC: 8342 AN: 68002

Other (OTH) AF: 0.0901 AC: 190 AN: 2108

Alfa AF: 0.113 Hom.: 2294

Bravo AF: 0.0986

Asia WGS AF: 0.147 AC: 511 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.5
DANN	Benign	0.57
PhyloP100		0.055

Splicing

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

Other links and lift over

dbSNP: rs8002852; hg19: chr13-108818885;