rs13149020

Positions:

• chr4-27192449-C-A
• chr4-27192449-C-T

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 0.304 in 151,626 control chromosomes in the GnomAD database, including 7,865 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 0.30 (7865 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.258

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.392 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: 0.305 AC: 46168 AN: 151514 Hom.: 7866 Cov.: 32

Gnomad AFR AF: 0.184

Gnomad AMI AF: 0.502

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.294

Gnomad EAS AF: 0.0679

Gnomad SAS AF: 0.217

Gnomad FIN AF: 0.382

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.396

Gnomad OTH AF: 0.318

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

GnomAD4 genome AF: 0.304 AC: 46156 AN: 151626 Hom.: 7865 Cov.: 32 AF XY: 0.298 AC XY: 22055 AN XY: 74084

Gnomad4 AFR AF: 0.184

Gnomad4 AMR AF: 0.265

Gnomad4 ASJ AF: 0.294

Gnomad4 EAS AF: 0.0679

Gnomad4 SAS AF: 0.216

Gnomad4 FIN AF: 0.382

Gnomad4 NFE AF: 0.396

Gnomad4 OTH AF: 0.314

Alfa AF: 0.330 Hom.: 1144

Bravo AF: 0.292

Asia WGS AF: 0.136 AC: 472 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.1
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13149020; hg19: chr4-27194071;