4-156558922-C-T

Variant names:

• chr4-156558922-C-T
• rs2090870

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 0.593 in 151,982 control chromosomes in the GnomAD database, including 27,409 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 0.59 (27409 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.632
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.626 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: 0.593 AC: 90021 AN: 151862 Hom.: 27382 Cov.: 32

Gnomad AFR AF: 0.604

Gnomad AMI AF: 0.741

Gnomad AMR AF: 0.492

Gnomad ASJ AF: 0.562

Gnomad EAS AF: 0.227

Gnomad SAS AF: 0.522

Gnomad FIN AF: 0.665

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.630

Gnomad OTH AF: 0.584

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

GnomAD4 genome AF: 0.593 AC: 90102 AN: 151982 Hom.: 27409 Cov.: 32 AF XY: 0.588 AC XY: 43687 AN XY: 74300

African (AFR) AF: 0.604 AC: 25020 AN: 41452

American (AMR) AF: 0.492 AC: 7506 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.562 AC: 1950 AN: 3470

East Asian (EAS) AF: 0.228 AC: 1174 AN: 5158

South Asian (SAS) AF: 0.522 AC: 2518 AN: 4820

European-Finnish (FIN) AF: 0.665 AC: 7028 AN: 10562

Middle Eastern (MID) AF: 0.555 AC: 162 AN: 292

European-Non Finnish (NFE) AF: 0.631 AC: 42841 AN: 67944

Other (OTH) AF: 0.582 AC: 1230 AN: 2114

Alfa AF: 0.614 Hom.: 67864

Bravo AF: 0.583

Asia WGS AF: 0.368 AC: 1285 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.93
DANN	Benign	0.27
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs2090870; hg19: chr4-157480074;