4-141520513-G-C

Variant names:

• chr4-141520513-G-C
• rs1402812

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.268 in 152,144 control chromosomes in the GnomAD database, including 6,710 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 0.27 (6710 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.484

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.454 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: 0.268 AC: 40744 AN: 152026 Hom.: 6680 Cov.: 33

Gnomad AFR AF: 0.459

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.296

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.216

Gnomad SAS AF: 0.190

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.262

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

GnomAD4 genome AF: 0.268 AC: 40840 AN: 152144 Hom.: 6710 Cov.: 33 AF XY: 0.265 AC XY: 19741 AN XY: 74372

Gnomad4 AFR AF: 0.460

Gnomad4 AMR AF: 0.296

Gnomad4 ASJ AF: 0.188

Gnomad4 EAS AF: 0.215

Gnomad4 SAS AF: 0.191

Gnomad4 FIN AF: 0.127

Gnomad4 NFE AF: 0.183

Gnomad4 OTH AF: 0.262

Alfa AF: 0.0972 Hom.: 134

Bravo AF: 0.288

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.77
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1402812; hg19: chr4-142441666;