chr5-56736057-C-A

Variant names:

• chr5-56736057-C-A
• rs889312

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.682 in 151,942 control chromosomes in the GnomAD database, including 35,558 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 0.68 (35558 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.23
• Publications: 259 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.43).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.712 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.682 AC: 103504 AN: 151824 Hom.: 35543 Cov.: 31

Gnomad AFR AF: 0.666

Gnomad AMI AF: 0.672

Gnomad AMR AF: 0.611

Gnomad ASJ AF: 0.682

Gnomad EAS AF: 0.450

Gnomad SAS AF: 0.612

Gnomad FIN AF: 0.767

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.717

Gnomad OTH AF: 0.673

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

GnomAD4 genome AF: 0.682 AC: 103549 AN: 151942 Hom.: 35558 Cov.: 31 AF XY: 0.678 AC XY: 50338 AN XY: 74262

African (AFR) AF: 0.665 AC: 27548 AN: 41412

American (AMR) AF: 0.610 AC: 9302 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.682 AC: 2368 AN: 3470

East Asian (EAS) AF: 0.450 AC: 2326 AN: 5166

South Asian (SAS) AF: 0.612 AC: 2944 AN: 4808

European-Finnish (FIN) AF: 0.767 AC: 8090 AN: 10548

Middle Eastern (MID) AF: 0.663 AC: 195 AN: 294

European-Non Finnish (NFE) AF: 0.717 AC: 48757 AN: 67980

Other (OTH) AF: 0.669 AC: 1410 AN: 2108

Alfa AF: 0.699 Hom.: 160582

Bravo AF: 0.668

Asia WGS AF: 0.548 AC: 1904 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.43
CADD	Benign	18
DANN	Benign	0.79
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs889312; hg19: chr5-56031884;