4-34594202-T-C

Variant names:

• chr4-34594202-T-C
• rs10023150

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 0.476 in 151,378 control chromosomes in the GnomAD database, including 21,158 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 0.48 (21158 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.231
• Publications: 2 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 (AFR) allele frequency at 95% confidence interval = 0.833 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: 0.476 AC: 71926 AN: 151262 Hom.: 21103 Cov.: 32

Gnomad AFR AF: 0.840

Gnomad AMI AF: 0.211

Gnomad AMR AF: 0.415

Gnomad ASJ AF: 0.279

Gnomad EAS AF: 0.324

Gnomad SAS AF: 0.357

Gnomad FIN AF: 0.382

Gnomad MID AF: 0.274

Gnomad NFE AF: 0.318

Gnomad OTH AF: 0.420

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

GnomAD4 genome AF: 0.476 AC: 72040 AN: 151378 Hom.: 21158 Cov.: 32 AF XY: 0.474 AC XY: 35062 AN XY: 73954

African (AFR) AF: 0.840 AC: 34790 AN: 41394

American (AMR) AF: 0.415 AC: 6280 AN: 15144

Ashkenazi Jewish (ASJ) AF: 0.279 AC: 965 AN: 3458

East Asian (EAS) AF: 0.323 AC: 1651 AN: 5118

South Asian (SAS) AF: 0.356 AC: 1716 AN: 4826

European-Finnish (FIN) AF: 0.382 AC: 3999 AN: 10472

Middle Eastern (MID) AF: 0.281 AC: 82 AN: 292

European-Non Finnish (NFE) AF: 0.318 AC: 21484 AN: 67662

Other (OTH) AF: 0.420 AC: 881 AN: 2100

Alfa AF: 0.362 Hom.: 41742

Bravo AF: 0.491

Asia WGS AF: 0.425 AC: 1474 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	0.084
DANN	Benign	0.65
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs10023150; hg19: chr4-34595824;