chr6-80826997-C-T

Variant names:

• chr6-80826997-C-T
• rs13193950

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.105 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

Gnomad4 AFR AF: 0.108

Gnomad4 AMR AF: 0.0649

Gnomad4 ASJ AF: 0.124

Gnomad4 EAS AF: 0.210

Gnomad4 SAS AF: 0.318

Gnomad4 FIN AF: 0.0821

Gnomad4 NFE AF: 0.0903

Gnomad4 OTH AF: 0.104

Alfa AF: 0.0983 Hom.: 1775

Bravo AF: 0.0992

Asia WGS AF: 0.253 AC: 880 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13193950; hg19: chr6-81536714;