rs10033019

Variant names:

• chr4-39390320-G-A
• rs10033019

Your query was ambiguous. Multiple possible variants found:

• chr4-39390320-G-A
• chr4-39390320-G-C
• chr4-39390320-G-T

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 0.502 in 151,814 control chromosomes in the GnomAD database, including 19,369 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 0.50 (19369 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.685
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.563 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: 0.501 AC: 76071 AN: 151696 Hom.: 19331 Cov.: 31

Gnomad AFR AF: 0.511

Gnomad AMI AF: 0.398

Gnomad AMR AF: 0.566

Gnomad ASJ AF: 0.561

Gnomad EAS AF: 0.545

Gnomad SAS AF: 0.581

Gnomad FIN AF: 0.414

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.483

Gnomad OTH AF: 0.512

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

GnomAD4 genome AF: 0.502 AC: 76160 AN: 151814 Hom.: 19369 Cov.: 31 AF XY: 0.505 AC XY: 37440 AN XY: 74172

African (AFR) AF: 0.512 AC: 21177 AN: 41384

American (AMR) AF: 0.567 AC: 8635 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.561 AC: 1947 AN: 3470

East Asian (EAS) AF: 0.545 AC: 2807 AN: 5152

South Asian (SAS) AF: 0.581 AC: 2794 AN: 4810

European-Finnish (FIN) AF: 0.414 AC: 4350 AN: 10514

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.483 AC: 32848 AN: 67942

Other (OTH) AF: 0.511 AC: 1077 AN: 2106

Alfa AF: 0.493 Hom.: 10342

Bravo AF: 0.512

Asia WGS AF: 0.512 AC: 1780 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.53
DANN	Benign	0.71
PhyloP100		-0.69

Splicing

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

Other links and lift over

dbSNP: rs10033019; hg19: chr4-39391940;