rs13178296

Positions:

• chr5-161704594-A-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 151,986 control chromosomes in the GnomAD database, including 24,691 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 (24691 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.804

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.635 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: 85494 AN: 151868 Hom.: 24689 Cov.: 31

Gnomad AFR AF: 0.481

Gnomad AMI AF: 0.525

Gnomad AMR AF: 0.509

Gnomad ASJ AF: 0.631

Gnomad EAS AF: 0.304

Gnomad SAS AF: 0.484

Gnomad FIN AF: 0.607

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.640

Gnomad OTH AF: 0.567

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

GnomAD4 genome AF: 0.563 AC: 85515 AN: 151986 Hom.: 24691 Cov.: 31 AF XY: 0.558 AC XY: 41471 AN XY: 74290

Gnomad4 AFR AF: 0.481

Gnomad4 AMR AF: 0.508

Gnomad4 ASJ AF: 0.631

Gnomad4 EAS AF: 0.304

Gnomad4 SAS AF: 0.483

Gnomad4 FIN AF: 0.607

Gnomad4 NFE AF: 0.640

Gnomad4 OTH AF: 0.561

Alfa AF: 0.623 Hom.: 59503

Bravo AF: 0.549

Asia WGS AF: 0.375 AC: 1305 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.0
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13178296; hg19: chr5-161131600; COSMIC: COSV50878831;