rs1902498

Variant names:

• chr4-154995423-C-T
• rs1902498

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 0.514 in 152,034 control chromosomes in the GnomAD database, including 23,746 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 0.51 (23746 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.458
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.851 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.514 AC: 78048 AN: 151916 Hom.: 23688 Cov.: 32

Gnomad AFR AF: 0.858

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.376

Gnomad ASJ AF: 0.481

Gnomad EAS AF: 0.561

Gnomad SAS AF: 0.365

Gnomad FIN AF: 0.406

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.365

Gnomad OTH AF: 0.487

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

GnomAD4 genome AF: 0.514 AC: 78151 AN: 152034 Hom.: 23746 Cov.: 32 AF XY: 0.514 AC XY: 38205 AN XY: 74336

African (AFR) AF: 0.858 AC: 35612 AN: 41492

American (AMR) AF: 0.375 AC: 5734 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.481 AC: 1667 AN: 3468

East Asian (EAS) AF: 0.561 AC: 2888 AN: 5144

South Asian (SAS) AF: 0.365 AC: 1763 AN: 4826

European-Finnish (FIN) AF: 0.406 AC: 4285 AN: 10560

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.365 AC: 24822 AN: 67948

Other (OTH) AF: 0.483 AC: 1022 AN: 2114

Alfa AF: 0.405 Hom.: 7429

Bravo AF: 0.526

Asia WGS AF: 0.454 AC: 1580 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.36
DANN	Benign	0.32
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs1902498; hg19: chr4-155916575;