rs1902491

Variant names:

• chr4-155134181-C-A
• rs1902491

Your query was ambiguous. Multiple possible variants found:

• chr4-155134181-C-A
• chr4-155134181-C-G
• chr4-155134181-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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;