chr4-43422435-G-A

Variant names:

• chr4-43422435-G-A
• rs2347043

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 0.095 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.214 AC: 8840 AN: 41348

American (AMR) AF: 0.111 AC: 1699 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0199 AC: 69 AN: 3466

East Asian (EAS) AF: 0.340 AC: 1752 AN: 5148

South Asian (SAS) AF: 0.0603 AC: 290 AN: 4810

European-Finnish (FIN) AF: 0.0547 AC: 576 AN: 10530

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0148 AC: 1009 AN: 67976

Other (OTH) AF: 0.0877 AC: 185 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.086
DANN	Benign	0.41
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs2347043; hg19: chr4-43424452;