4-141520513-G-C

Variant names:

• chr4-141520513-G-C
• rs1402812

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 0.268 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.460 AC: 19075 AN: 41488

American (AMR) AF: 0.296 AC: 4531 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.188 AC: 652 AN: 3472

East Asian (EAS) AF: 0.215 AC: 1112 AN: 5166

South Asian (SAS) AF: 0.191 AC: 921 AN: 4828

European-Finnish (FIN) AF: 0.127 AC: 1345 AN: 10594

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.183 AC: 12471 AN: 67994

Other (OTH) AF: 0.262 AC: 553 AN: 2112

Alfa AF: 0.0972 Hom.: 134

Bravo AF: 0.288

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.77
DANN	Benign	0.45
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs1402812; hg19: chr4-142441666;