rs2347043

chr4-43422435-G-A

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 0.095 in 151,864 control chromosomes in the GnomAD database, including 1,423 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 0.095 (1423 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.327 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0949 AC: 14395 AN: 151746 Hom.: 1416 Cov.: 32

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.0199

Gnomad EAS AF: 0.341

Gnomad SAS AF: 0.0607

Gnomad FIN AF: 0.0547

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0148

Gnomad OTH AF: 0.0862

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

GnomAD4 genome AF: 0.0950 AC: 14434 AN: 151864 Hom.: 1423 Cov.: 32 AF XY: 0.0978 AC XY: 7255 AN XY: 74206

Gnomad4 AFR AF: 0.214

Gnomad4 AMR AF: 0.111

Gnomad4 ASJ AF: 0.0199

Gnomad4 EAS AF: 0.340

Gnomad4 SAS AF: 0.0603

Gnomad4 FIN AF: 0.0547

Gnomad4 NFE AF: 0.0148

Gnomad4 OTH AF: 0.0877

Alfa AF: 0.0703 Hom.: 155

Bravo AF: 0.106

Asia WGS AF: 0.207 AC: 717 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.086
Dann	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2347043; hg19: chr4-43424452;