chr6-56029181-A-G

Variant names:

• chr6-56029181-A-G
• rs2206682

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 152,032 control chromosomes in the GnomAD database, including 43,008 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 (43008 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0490
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.903 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: 0.742 AC: 112793 AN: 151912 Hom.: 42963 Cov.: 31

Gnomad AFR AF: 0.910

Gnomad AMI AF: 0.540

Gnomad AMR AF: 0.674

Gnomad ASJ AF: 0.744

Gnomad EAS AF: 0.921

Gnomad SAS AF: 0.772

Gnomad FIN AF: 0.638

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.660

Gnomad OTH AF: 0.708

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

GnomAD4 genome AF: 0.743 AC: 112892 AN: 152032 Hom.: 43008 Cov.: 31 AF XY: 0.740 AC XY: 54960 AN XY: 74298

African (AFR) AF: 0.910 AC: 37786 AN: 41508

American (AMR) AF: 0.675 AC: 10302 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.744 AC: 2580 AN: 3470

East Asian (EAS) AF: 0.921 AC: 4751 AN: 5158

South Asian (SAS) AF: 0.771 AC: 3715 AN: 4818

European-Finnish (FIN) AF: 0.638 AC: 6718 AN: 10530

Middle Eastern (MID) AF: 0.728 AC: 214 AN: 294

European-Non Finnish (NFE) AF: 0.660 AC: 44854 AN: 67962

Other (OTH) AF: 0.702 AC: 1482 AN: 2112

Alfa AF: 0.696 Hom.: 19604

Bravo AF: 0.751

Asia WGS AF: 0.818 AC: 2844 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.0
DANN	Benign	0.79
PhyloP100		0.049

Splicing

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

Other links and lift over

dbSNP: rs2206682; hg19: chr6-55893979;