6-56028999-G-A

Variant names:

• chr6-56028999-G-A
• rs2223662

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 0.743 in 152,014 control chromosomes in the GnomAD database, including 43,010 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 0.74 (43010 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.20
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.903 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.743 AC: 112793 AN: 151896 Hom.: 42965 Cov.: 31

Gnomad AFR AF: 0.910

Gnomad AMI AF: 0.539

Gnomad AMR AF: 0.674

Gnomad ASJ AF: 0.743

Gnomad EAS AF: 0.921

Gnomad SAS AF: 0.773

Gnomad FIN AF: 0.639

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.660

Gnomad OTH AF: 0.707

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

GnomAD4 genome AF: 0.743 AC: 112891 AN: 152014 Hom.: 43010 Cov.: 31 AF XY: 0.740 AC XY: 54989 AN XY: 74312

African (AFR) AF: 0.911 AC: 37786 AN: 41498

American (AMR) AF: 0.674 AC: 10282 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.743 AC: 2578 AN: 3468

East Asian (EAS) AF: 0.921 AC: 4756 AN: 5162

South Asian (SAS) AF: 0.773 AC: 3721 AN: 4816

European-Finnish (FIN) AF: 0.639 AC: 6737 AN: 10550

Middle Eastern (MID) AF: 0.731 AC: 215 AN: 294

European-Non Finnish (NFE) AF: 0.660 AC: 44842 AN: 67954

Other (OTH) AF: 0.701 AC: 1482 AN: 2114

Alfa AF: 0.675 Hom.: 56411

Bravo AF: 0.751

Asia WGS AF: 0.819 AC: 2845 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.12
DANN	Benign	0.42
PhyloP100		-3.2

Splicing

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

Other links and lift over

dbSNP: rs2223662; hg19: chr6-55893797;