2-17857545-A-G

Variant names:

• chr2-17857545-A-G
• rs6758546

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 0.825 in 151,064 control chromosomes in the GnomAD database, including 52,180 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 0.83 (52180 hom., cov: 27)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.78
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.886 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: 0.825 AC: 124592 AN: 150946 Hom.: 52136 Cov.: 27

Gnomad AFR AF: 0.679

Gnomad AMI AF: 0.997

Gnomad AMR AF: 0.898

Gnomad ASJ AF: 0.861

Gnomad EAS AF: 0.750

Gnomad SAS AF: 0.826

Gnomad FIN AF: 0.879

Gnomad MID AF: 0.899

Gnomad NFE AF: 0.890

Gnomad OTH AF: 0.855

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

GnomAD4 genome AF: 0.825 AC: 124688 AN: 151064 Hom.: 52180 Cov.: 27 AF XY: 0.827 AC XY: 60925 AN XY: 73702

African (AFR) AF: 0.679 AC: 27895 AN: 41086

American (AMR) AF: 0.899 AC: 13625 AN: 15164

Ashkenazi Jewish (ASJ) AF: 0.861 AC: 2989 AN: 3470

East Asian (EAS) AF: 0.750 AC: 3780 AN: 5038

South Asian (SAS) AF: 0.827 AC: 3958 AN: 4786

European-Finnish (FIN) AF: 0.879 AC: 9051 AN: 10300

Middle Eastern (MID) AF: 0.908 AC: 267 AN: 294

European-Non Finnish (NFE) AF: 0.890 AC: 60416 AN: 67910

Other (OTH) AF: 0.855 AC: 1798 AN: 2104

Alfa AF: 0.869 Hom.: 64415

Bravo AF: 0.818

Asia WGS AF: 0.777 AC: 2703 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
DANN	Benign	0.62
PhyloP100		-2.8

Splicing

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

Other links and lift over

dbSNP: rs6758546; hg19: chr2-18038812;