rs6726177

Variant names:

• chr2-106331461-G-A
• rs6726177

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 0.806 in 152,186 control chromosomes in the GnomAD database, including 49,669 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 0.81 (49669 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.943 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: 0.806 AC: 122507 AN: 152068 Hom.: 49621 Cov.: 32

Gnomad AFR AF: 0.740

Gnomad AMI AF: 0.956

Gnomad AMR AF: 0.842

Gnomad ASJ AF: 0.803

Gnomad EAS AF: 0.966

Gnomad SAS AF: 0.857

Gnomad FIN AF: 0.877

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.809

Gnomad OTH AF: 0.792

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

GnomAD4 genome AF: 0.806 AC: 122615 AN: 152186 Hom.: 49669 Cov.: 32 AF XY: 0.811 AC XY: 60354 AN XY: 74404

African (AFR) AF: 0.741 AC: 30746 AN: 41502

American (AMR) AF: 0.842 AC: 12871 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.803 AC: 2787 AN: 3470

East Asian (EAS) AF: 0.966 AC: 4992 AN: 5170

South Asian (SAS) AF: 0.857 AC: 4132 AN: 4824

European-Finnish (FIN) AF: 0.877 AC: 9302 AN: 10604

Middle Eastern (MID) AF: 0.820 AC: 241 AN: 294

European-Non Finnish (NFE) AF: 0.809 AC: 55003 AN: 68026

Other (OTH) AF: 0.793 AC: 1671 AN: 2108

Alfa AF: 0.807 Hom.: 47242

Bravo AF: 0.800

Asia WGS AF: 0.897 AC: 3116 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.024
DANN	Benign	0.15
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs6726177; hg19: chr2-106947917;