chr6-80826285-A-C

Variant names:

• chr6-80826285-A-C
• rs16892285

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 151,908 control chromosomes in the GnomAD database, including 1,006 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 (1006 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00500
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.304 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: 15866 AN: 151790 Hom.: 1002 Cov.: 31

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.164

Gnomad AMR AF: 0.0648

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.207

Gnomad SAS AF: 0.317

Gnomad FIN AF: 0.0818

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0903

Gnomad OTH AF: 0.103

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

GnomAD4 genome AF: 0.105 AC: 15878 AN: 151908 Hom.: 1006 Cov.: 31 AF XY: 0.109 AC XY: 8091 AN XY: 74252

African (AFR) AF: 0.108 AC: 4471 AN: 41450

American (AMR) AF: 0.0647 AC: 986 AN: 15238

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

East Asian (EAS) AF: 0.207 AC: 1060 AN: 5122

South Asian (SAS) AF: 0.317 AC: 1526 AN: 4810

European-Finnish (FIN) AF: 0.0818 AC: 864 AN: 10566

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

European-Non Finnish (NFE) AF: 0.0903 AC: 6137 AN: 67936

Other (OTH) AF: 0.104 AC: 220 AN: 2116

Alfa AF: 0.0962 Hom.: 125

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	-0.92
CADD	Benign	0.91
DANN	Benign	0.69
PhyloP100		0.0050

Splicing

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

Other links and lift over

dbSNP: rs16892285; hg19: chr6-81536002;