rs13109457

chr4-154593727-G-Achr4-154593727-G-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 0.257 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.236

Gnomad4 AMR AF: 0.233

Gnomad4 ASJ AF: 0.187

Gnomad4 EAS AF: 0.441

Gnomad4 SAS AF: 0.303

Gnomad4 FIN AF: 0.311

Gnomad4 NFE AF: 0.254

Gnomad4 OTH AF: 0.228

Alfa AF: 0.244 Hom.: 5724

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13109457; hg19: chr4-155514879;