5-2806755-A-G

Variant names:

• chr5-2806755-A-G
• rs12187040

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 0.772 in 152,152 control chromosomes in the GnomAD database, including 46,185 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 0.77 (46185 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.31
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.887 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: 0.773 AC: 117479 AN: 152034 Hom.: 46181 Cov.: 33

Gnomad AFR AF: 0.612

Gnomad AMI AF: 0.840

Gnomad AMR AF: 0.844

Gnomad ASJ AF: 0.819

Gnomad EAS AF: 0.910

Gnomad SAS AF: 0.843

Gnomad FIN AF: 0.848

Gnomad MID AF: 0.839

Gnomad NFE AF: 0.823

Gnomad OTH AF: 0.802

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

GnomAD4 genome AF: 0.772 AC: 117524 AN: 152152 Hom.: 46185 Cov.: 33 AF XY: 0.778 AC XY: 57827 AN XY: 74362

African (AFR) AF: 0.612 AC: 25403 AN: 41502

American (AMR) AF: 0.844 AC: 12916 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.819 AC: 2842 AN: 3468

East Asian (EAS) AF: 0.909 AC: 4673 AN: 5140

South Asian (SAS) AF: 0.842 AC: 4062 AN: 4824

European-Finnish (FIN) AF: 0.848 AC: 8994 AN: 10604

Middle Eastern (MID) AF: 0.837 AC: 246 AN: 294

European-Non Finnish (NFE) AF: 0.823 AC: 55934 AN: 67996

Other (OTH) AF: 0.798 AC: 1688 AN: 2114

Alfa AF: 0.774 Hom.: 4079

Bravo AF: 0.765

Asia WGS AF: 0.853 AC: 2968 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	0.63
DANN	Benign	0.25
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs12187040; hg19: chr5-2806869;