chr6-80806319-A-C

Variant names:

• chr6-80806319-A-C
• rs13213247

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 0.0724 in 151,390 control chromosomes in the GnomAD database, including 523 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 0.072 (523 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.986
• Publications: 5 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 (EAS) allele frequency at 95% confidence interval = 0.177 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: 0.0723 AC: 10937 AN: 151272 Hom.: 518 Cov.: 31

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.0802

Gnomad AMR AF: 0.0677

Gnomad ASJ AF: 0.0751

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.158

Gnomad FIN AF: 0.0419

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0440

Gnomad OTH AF: 0.0638

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

GnomAD4 genome AF: 0.0724 AC: 10961 AN: 151390 Hom.: 523 Cov.: 31 AF XY: 0.0749 AC XY: 5541 AN XY: 73972

African (AFR) AF: 0.104 AC: 4305 AN: 41414

American (AMR) AF: 0.0685 AC: 1036 AN: 15124

Ashkenazi Jewish (ASJ) AF: 0.0751 AC: 260 AN: 3462

East Asian (EAS) AF: 0.187 AC: 953 AN: 5090

South Asian (SAS) AF: 0.158 AC: 762 AN: 4818

European-Finnish (FIN) AF: 0.0419 AC: 443 AN: 10578

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0440 AC: 2973 AN: 67594

Other (OTH) AF: 0.0651 AC: 137 AN: 2106

Alfa AF: 0.0494 Hom.: 94

Bravo AF: 0.0736

Asia WGS AF: 0.164 AC: 568 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.6
DANN	Benign	0.65
PhyloP100		-0.99

Splicing

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

Other links and lift over

dbSNP: rs13213247; hg19: chr6-81516036;