rs13178362

Variant names:

• chr5-30178906-T-C
• rs13178362

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 0.164 in 151,886 control chromosomes in the GnomAD database, including 2,148 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 0.16 (2148 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.451
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.189 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: 0.164 AC: 24943 AN: 151776 Hom.: 2141 Cov.: 32

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.0768

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.0524

Gnomad SAS AF: 0.158

Gnomad FIN AF: 0.233

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.159

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

GnomAD4 genome AF: 0.164 AC: 24984 AN: 151886 Hom.: 2148 Cov.: 32 AF XY: 0.167 AC XY: 12403 AN XY: 74208

African (AFR) AF: 0.157 AC: 6494 AN: 41460

American (AMR) AF: 0.195 AC: 2978 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.151 AC: 526 AN: 3472

East Asian (EAS) AF: 0.0519 AC: 268 AN: 5164

South Asian (SAS) AF: 0.158 AC: 763 AN: 4818

European-Finnish (FIN) AF: 0.233 AC: 2445 AN: 10490

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.163 AC: 11044 AN: 67922

Other (OTH) AF: 0.161 AC: 340 AN: 2108

Alfa AF: 0.160 Hom.: 3584

Bravo AF: 0.161

Asia WGS AF: 0.122 AC: 422 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	7.9
DANN	Benign	0.77
PhyloP100		0.45

Splicing

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

Other links and lift over

dbSNP: rs13178362; hg19: chr5-30179013;