chr4-186567219-T-A

Variant names:

• chr4-186567219-T-A
• rs12642043

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 0.586 in 151,972 control chromosomes in the GnomAD database, including 26,307 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 (26307 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.29

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.612 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: 0.586 AC: 88944 AN: 151852 Hom.: 26281 Cov.: 31

Gnomad AFR AF: 0.560

Gnomad AMI AF: 0.691

Gnomad AMR AF: 0.567

Gnomad ASJ AF: 0.618

Gnomad EAS AF: 0.387

Gnomad SAS AF: 0.456

Gnomad FIN AF: 0.646

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.617

Gnomad OTH AF: 0.598

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

GnomAD4 genome AF: 0.586 AC: 89021 AN: 151972 Hom.: 26307 Cov.: 31 AF XY: 0.584 AC XY: 43344 AN XY: 74272

Gnomad4 AFR AF: 0.560

Gnomad4 AMR AF: 0.566

Gnomad4 ASJ AF: 0.618

Gnomad4 EAS AF: 0.388

Gnomad4 SAS AF: 0.457

Gnomad4 FIN AF: 0.646

Gnomad4 NFE AF: 0.617

Gnomad4 OTH AF: 0.599

Alfa AF: 0.598 Hom.: 3427

Bravo AF: 0.578

Asia WGS AF: 0.461 AC: 1602 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.40
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12642043; hg19: chr4-187488373;