rs6519166

Variant names:

• chr22-39076172-C-A
• rs6519166

Your query was ambiguous. Multiple possible variants found:

• chr22-39076172-C-A
• chr22-39076172-C-T

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 0.679 in 151,592 control chromosomes in the GnomAD database, including 35,076 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 0.68 (35076 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.42
• Publications: 14 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.733 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: 0.679 AC: 102811 AN: 151472 Hom.: 35044 Cov.: 31

Gnomad AFR AF: 0.711

Gnomad AMI AF: 0.591

Gnomad AMR AF: 0.744

Gnomad ASJ AF: 0.672

Gnomad EAS AF: 0.751

Gnomad SAS AF: 0.609

Gnomad FIN AF: 0.555

Gnomad MID AF: 0.675

Gnomad NFE AF: 0.664

Gnomad OTH AF: 0.708

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

GnomAD4 genome AF: 0.679 AC: 102893 AN: 151592 Hom.: 35076 Cov.: 31 AF XY: 0.673 AC XY: 49873 AN XY: 74052

African (AFR) AF: 0.710 AC: 29392 AN: 41376

American (AMR) AF: 0.744 AC: 11333 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.672 AC: 2327 AN: 3462

East Asian (EAS) AF: 0.751 AC: 3847 AN: 5122

South Asian (SAS) AF: 0.607 AC: 2919 AN: 4806

European-Finnish (FIN) AF: 0.555 AC: 5810 AN: 10474

Middle Eastern (MID) AF: 0.678 AC: 198 AN: 292

European-Non Finnish (NFE) AF: 0.664 AC: 45035 AN: 67818

Other (OTH) AF: 0.711 AC: 1497 AN: 2106

Alfa AF: 0.578 Hom.: 1770

Bravo AF: 0.698

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.31
DANN	Benign	0.45
PhyloP100		-2.4
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs6519166; hg19: chr22-39472177;