rs1902491

chr4-155134181-C-Achr4-155134181-C-Gchr4-155134181-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 0.426 in 151,852 control chromosomes in the GnomAD database, including 14,539 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 0.43 (14539 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.890

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.805 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: 0.426 AC: 64709 AN: 151734 Hom.: 14527 Cov.: 32

Gnomad AFR AF: 0.381

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.471

Gnomad ASJ AF: 0.413

Gnomad EAS AF: 0.825

Gnomad SAS AF: 0.543

Gnomad FIN AF: 0.555

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.389

Gnomad OTH AF: 0.427

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

GnomAD4 genome AF: 0.426 AC: 64764 AN: 151852 Hom.: 14539 Cov.: 32 AF XY: 0.439 AC XY: 32549 AN XY: 74150

Gnomad4 AFR AF: 0.381

Gnomad4 AMR AF: 0.471

Gnomad4 ASJ AF: 0.413

Gnomad4 EAS AF: 0.825

Gnomad4 SAS AF: 0.543

Gnomad4 FIN AF: 0.555

Gnomad4 NFE AF: 0.389

Gnomad4 OTH AF: 0.430

Alfa AF: 0.382 Hom.: 6448

Bravo AF: 0.416

Asia WGS AF: 0.673 AC: 2339 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	0.63
Dann	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1902491; hg19: chr4-156055333;