4-51832591-T-C

Variant names:

• chr4-51832591-T-C
• rs1910740

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 0.418 in 151,920 control chromosomes in the GnomAD database, including 16,006 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 (16006 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.297
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.697 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: 0.418 AC: 63441 AN: 151802 Hom.: 15984 Cov.: 32

Gnomad AFR AF: 0.704

Gnomad AMI AF: 0.238

Gnomad AMR AF: 0.296

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.636

Gnomad SAS AF: 0.473

Gnomad FIN AF: 0.325

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.278

Gnomad OTH AF: 0.352

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

GnomAD4 genome AF: 0.418 AC: 63523 AN: 151920 Hom.: 16006 Cov.: 32 AF XY: 0.420 AC XY: 31179 AN XY: 74270

African (AFR) AF: 0.704 AC: 29178 AN: 41450

American (AMR) AF: 0.296 AC: 4526 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.270 AC: 936 AN: 3466

East Asian (EAS) AF: 0.636 AC: 3254 AN: 5114

South Asian (SAS) AF: 0.471 AC: 2269 AN: 4816

European-Finnish (FIN) AF: 0.325 AC: 3432 AN: 10560

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.278 AC: 18896 AN: 67928

Other (OTH) AF: 0.355 AC: 751 AN: 2114

Alfa AF: 0.289 Hom.: 3824

Bravo AF: 0.426

Asia WGS AF: 0.541 AC: 1880 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.6
DANN	Benign	0.79
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs1910740; hg19: chr4-52698757;