rs13178296

Variant names:

• chr5-161704594-A-C
• rs13178296

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 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.481 AC: 19930 AN: 41474

American (AMR) AF: 0.508 AC: 7743 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.631 AC: 2188 AN: 3468

East Asian (EAS) AF: 0.304 AC: 1568 AN: 5160

South Asian (SAS) AF: 0.483 AC: 2323 AN: 4812

European-Finnish (FIN) AF: 0.607 AC: 6409 AN: 10556

Middle Eastern (MID) AF: 0.588 AC: 173 AN: 294

European-Non Finnish (NFE) AF: 0.640 AC: 43520 AN: 67954

Other (OTH) AF: 0.561 AC: 1184 AN: 2112

Alfa AF: 0.611 Hom.: 90845

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
PhyloP100		0.80

Splicing

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

Other links and lift over

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