rs13356727

Positions:

• chr5-1312342-G-A
• chr5-1312342-G-C

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	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

Gnomad4 AFR AF: 0.430

Gnomad4 AMR AF: 0.680

Gnomad4 ASJ AF: 0.577

Gnomad4 EAS AF: 0.816

Gnomad4 SAS AF: 0.807

Gnomad4 FIN AF: 0.536

Gnomad4 NFE AF: 0.584

Gnomad4 OTH AF: 0.589

Alfa AF: 0.578 Hom.: 6044

Bravo AF: 0.564

Asia WGS AF: 0.771 AC: 2681 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

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