rs13193950

Variant names:

• chr6-80826997-C-T
• rs13193950

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 0.105 in 151,998 control chromosomes in the GnomAD database, including 1,012 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 0.10 (1012 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.594
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.305 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.105 AC: 15914 AN: 151880 Hom.: 1008 Cov.: 32

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.163

Gnomad AMR AF: 0.0649

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.209

Gnomad SAS AF: 0.318

Gnomad FIN AF: 0.0821

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0903

Gnomad OTH AF: 0.104

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

GnomAD4 genome AF: 0.105 AC: 15926 AN: 151998 Hom.: 1012 Cov.: 32 AF XY: 0.109 AC XY: 8121 AN XY: 74298

African (AFR) AF: 0.108 AC: 4487 AN: 41492

American (AMR) AF: 0.0649 AC: 988 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.124 AC: 431 AN: 3468

East Asian (EAS) AF: 0.210 AC: 1076 AN: 5134

South Asian (SAS) AF: 0.318 AC: 1533 AN: 4816

European-Finnish (FIN) AF: 0.0821 AC: 869 AN: 10588

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.0903 AC: 6139 AN: 67952

Other (OTH) AF: 0.104 AC: 220 AN: 2108

Alfa AF: 0.0983 Hom.: 3502

Bravo AF: 0.0992

Asia WGS AF: 0.253 AC: 880 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.9
DANN	Benign	0.48
PhyloP100		0.59

Splicing

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

Other links and lift over

dbSNP: rs13193950; hg19: chr6-81536714;