rs13147579

Variant names:

• chr4-154527896-C-T
• rs13147579

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 0.196 in 152,160 control chromosomes in the GnomAD database, including 3,479 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 0.20 (3479 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0800
• Publications: 2 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 = 0.534 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: 0.196 AC: 29841 AN: 152042 Hom.: 3478 Cov.: 32

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.316

Gnomad AMR AF: 0.217

Gnomad ASJ AF: 0.167

Gnomad EAS AF: 0.551

Gnomad SAS AF: 0.234

Gnomad FIN AF: 0.258

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.198

Gnomad OTH AF: 0.190

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

GnomAD4 genome AF: 0.196 AC: 29854 AN: 152160 Hom.: 3479 Cov.: 32 AF XY: 0.203 AC XY: 15065 AN XY: 74370

African (AFR) AF: 0.122 AC: 5046 AN: 41520

American (AMR) AF: 0.217 AC: 3321 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.167 AC: 580 AN: 3470

East Asian (EAS) AF: 0.551 AC: 2849 AN: 5170

South Asian (SAS) AF: 0.235 AC: 1130 AN: 4818

European-Finnish (FIN) AF: 0.258 AC: 2723 AN: 10568

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.198 AC: 13473 AN: 68002

Other (OTH) AF: 0.189 AC: 400 AN: 2114

Alfa AF: 0.163 Hom.: 522

Bravo AF: 0.192

Asia WGS AF: 0.339 AC: 1176 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	2.8
DANN	Benign	0.54
PhyloP100		-0.080

Splicing

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

Other links and lift over

dbSNP: rs13147579; hg19: chr4-155449048;