4-155400731-C-T

Variant names:

• chr4-155400731-C-T
• rs1517290

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 0.419 in 151,702 control chromosomes in the GnomAD database, including 14,257 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 0.42 (14257 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.855 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.419 AC: 63555 AN: 151582 Hom.: 14249 Cov.: 32

Gnomad AFR AF: 0.332

Gnomad AMI AF: 0.513

Gnomad AMR AF: 0.437

Gnomad ASJ AF: 0.359

Gnomad EAS AF: 0.877

Gnomad SAS AF: 0.563

Gnomad FIN AF: 0.519

Gnomad MID AF: 0.366

Gnomad NFE AF: 0.411

Gnomad OTH AF: 0.407

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

GnomAD4 genome AF: 0.419 AC: 63606 AN: 151702 Hom.: 14257 Cov.: 32 AF XY: 0.430 AC XY: 31864 AN XY: 74132

African (AFR) AF: 0.332 AC: 13725 AN: 41364

American (AMR) AF: 0.438 AC: 6677 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.359 AC: 1245 AN: 3464

East Asian (EAS) AF: 0.877 AC: 4487 AN: 5118

South Asian (SAS) AF: 0.563 AC: 2709 AN: 4810

European-Finnish (FIN) AF: 0.519 AC: 5449 AN: 10490

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.411 AC: 27874 AN: 67888

Other (OTH) AF: 0.411 AC: 868 AN: 2110

Alfa AF: 0.420 Hom.: 1785

Bravo AF: 0.407

Asia WGS AF: 0.687 AC: 2386 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.8
DANN	Benign	0.42
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs1517290; hg19: chr4-156321883;