4-34892233-A-G

Variant names:

• chr4-34892233-A-G
• rs17390445

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 0.597 in 151,808 control chromosomes in the GnomAD database, including 28,654 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 0.60 (28654 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347
• Publications: 19 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.898 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: 0.597 AC: 90604 AN: 151690 Hom.: 28630 Cov.: 31

Gnomad AFR AF: 0.382

Gnomad AMI AF: 0.661

Gnomad AMR AF: 0.694

Gnomad ASJ AF: 0.643

Gnomad EAS AF: 0.920

Gnomad SAS AF: 0.770

Gnomad FIN AF: 0.651

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.658

Gnomad OTH AF: 0.605

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

GnomAD4 genome AF: 0.597 AC: 90668 AN: 151808 Hom.: 28654 Cov.: 31 AF XY: 0.604 AC XY: 44828 AN XY: 74202

African (AFR) AF: 0.382 AC: 15815 AN: 41406

American (AMR) AF: 0.694 AC: 10591 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.643 AC: 2228 AN: 3464

East Asian (EAS) AF: 0.920 AC: 4760 AN: 5174

South Asian (SAS) AF: 0.772 AC: 3705 AN: 4802

European-Finnish (FIN) AF: 0.651 AC: 6835 AN: 10502

Middle Eastern (MID) AF: 0.626 AC: 184 AN: 294

European-Non Finnish (NFE) AF: 0.658 AC: 44679 AN: 67906

Other (OTH) AF: 0.604 AC: 1268 AN: 2098

Alfa AF: 0.658 Hom.: 53394

Bravo AF: 0.588

Asia WGS AF: 0.766 AC: 2651 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.4
DANN	Benign	0.38
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs17390445; hg19: chr4-34893855;