4-183772921-C-T

Variant names:

• chr4-183772921-C-T
• rs4129955

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 0.474 in 151,972 control chromosomes in the GnomAD database, including 17,376 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 0.47 (17376 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.189
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.666 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: 0.474 AC: 71927 AN: 151854 Hom.: 17360 Cov.: 31

Gnomad AFR AF: 0.501

Gnomad AMI AF: 0.566

Gnomad AMR AF: 0.420

Gnomad ASJ AF: 0.511

Gnomad EAS AF: 0.685

Gnomad SAS AF: 0.550

Gnomad FIN AF: 0.367

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.461

Gnomad OTH AF: 0.485

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

GnomAD4 genome AF: 0.474 AC: 71974 AN: 151972 Hom.: 17376 Cov.: 31 AF XY: 0.469 AC XY: 34844 AN XY: 74274

African (AFR) AF: 0.501 AC: 20750 AN: 41428

American (AMR) AF: 0.420 AC: 6422 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.511 AC: 1773 AN: 3472

East Asian (EAS) AF: 0.685 AC: 3533 AN: 5158

South Asian (SAS) AF: 0.551 AC: 2646 AN: 4806

European-Finnish (FIN) AF: 0.367 AC: 3877 AN: 10572

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.461 AC: 31311 AN: 67950

Other (OTH) AF: 0.483 AC: 1016 AN: 2104

Alfa AF: 0.465 Hom.: 28159

Bravo AF: 0.480

Asia WGS AF: 0.571 AC: 1986 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.63
DANN	Benign	0.33
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs4129955; hg19: chr4-184694074;