chr5-1312342-G-A

Variant names:

• chr5-1312342-G-A
• rs13356727

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 0.563 in 152,136 control chromosomes in the GnomAD database, including 25,023 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 0.56 (25023 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.336
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.796 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.563 AC: 85563 AN: 152018 Hom.: 25012 Cov.: 33

Gnomad AFR AF: 0.430

Gnomad AMI AF: 0.533

Gnomad AMR AF: 0.680

Gnomad ASJ AF: 0.577

Gnomad EAS AF: 0.816

Gnomad SAS AF: 0.806

Gnomad FIN AF: 0.536

Gnomad MID AF: 0.580

Gnomad NFE AF: 0.584

Gnomad OTH AF: 0.588

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

GnomAD4 genome AF: 0.563 AC: 85614 AN: 152136 Hom.: 25023 Cov.: 33 AF XY: 0.570 AC XY: 42420 AN XY: 74368

African (AFR) AF: 0.430 AC: 17847 AN: 41502

American (AMR) AF: 0.680 AC: 10398 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.577 AC: 2001 AN: 3470

East Asian (EAS) AF: 0.816 AC: 4227 AN: 5178

South Asian (SAS) AF: 0.807 AC: 3897 AN: 4828

European-Finnish (FIN) AF: 0.536 AC: 5670 AN: 10584

Middle Eastern (MID) AF: 0.562 AC: 164 AN: 292

European-Non Finnish (NFE) AF: 0.584 AC: 39678 AN: 67970

Other (OTH) AF: 0.589 AC: 1246 AN: 2114

Alfa AF: 0.580 Hom.: 11173

Bravo AF: 0.564

Asia WGS AF: 0.771 AC: 2681 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.7
DANN	Benign	0.49
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs13356727; hg19: chr5-1312457; COSMIC: COSV73867971;