rs2206682

chr6-56029181-A-Gchr6-56029181-A-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.910

Gnomad4 AMR AF: 0.675

Gnomad4 ASJ AF: 0.744

Gnomad4 EAS AF: 0.921

Gnomad4 SAS AF: 0.771

Gnomad4 FIN AF: 0.638

Gnomad4 NFE AF: 0.660

Gnomad4 OTH AF: 0.702

Alfa AF: 0.699 Hom.: 17853

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2206682; hg19: chr6-55893979;