rs13109457

Variant names:

• chr4-154593727-G-A
• rs13109457

Your query was ambiguous. Multiple possible variants found:

• chr4-154593727-G-A
• chr4-154593727-G-T

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 0.257 in 151,830 control chromosomes in the GnomAD database, including 5,168 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 0.26 (5168 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.421
• Publications: 22 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.426 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: 0.257 AC: 38991 AN: 151712 Hom.: 5166 Cov.: 31

Gnomad AFR AF: 0.236

Gnomad AMI AF: 0.254

Gnomad AMR AF: 0.233

Gnomad ASJ AF: 0.187

Gnomad EAS AF: 0.441

Gnomad SAS AF: 0.302

Gnomad FIN AF: 0.311

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.230

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

GnomAD4 genome AF: 0.257 AC: 39004 AN: 151830 Hom.: 5168 Cov.: 31 AF XY: 0.259 AC XY: 19217 AN XY: 74188

African (AFR) AF: 0.236 AC: 9780 AN: 41382

American (AMR) AF: 0.233 AC: 3558 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.187 AC: 649 AN: 3468

East Asian (EAS) AF: 0.441 AC: 2265 AN: 5134

South Asian (SAS) AF: 0.303 AC: 1457 AN: 4812

European-Finnish (FIN) AF: 0.311 AC: 3268 AN: 10510

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.254 AC: 17258 AN: 67938

Other (OTH) AF: 0.228 AC: 481 AN: 2108

Alfa AF: 0.248 Hom.: 10177

Bravo AF: 0.252

Asia WGS AF: 0.315 AC: 1093 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.7
DANN	Benign	0.56
PhyloP100		0.42

Splicing

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

Other links and lift over

dbSNP: rs13109457; hg19: chr4-155514879;