rs10033464

Variant names:

• chr4-110799605-T-G
• rs10033464

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.859 in 152,214 control chromosomes in the GnomAD database, including 56,312 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 0.86 (56312 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.849
• Publications: 141 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.36).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.898 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: 0.859 AC: 130653 AN: 152096 Hom.: 56272 Cov.: 34

Gnomad AFR AF: 0.819

Gnomad AMI AF: 0.936

Gnomad AMR AF: 0.817

Gnomad ASJ AF: 0.925

Gnomad EAS AF: 0.773

Gnomad SAS AF: 0.782

Gnomad FIN AF: 0.832

Gnomad MID AF: 0.908

Gnomad NFE AF: 0.904

Gnomad OTH AF: 0.874

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

GnomAD4 genome AF: 0.859 AC: 130752 AN: 152214 Hom.: 56312 Cov.: 34 AF XY: 0.851 AC XY: 63341 AN XY: 74424

African (AFR) AF: 0.819 AC: 34030 AN: 41534

American (AMR) AF: 0.817 AC: 12490 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.925 AC: 3212 AN: 3472

East Asian (EAS) AF: 0.773 AC: 3998 AN: 5170

South Asian (SAS) AF: 0.782 AC: 3778 AN: 4832

European-Finnish (FIN) AF: 0.832 AC: 8799 AN: 10578

Middle Eastern (MID) AF: 0.915 AC: 269 AN: 294

European-Non Finnish (NFE) AF: 0.904 AC: 61476 AN: 68020

Other (OTH) AF: 0.872 AC: 1846 AN: 2116

Alfa AF: 0.892 Hom.: 208134

Bravo AF: 0.859

Asia WGS AF: 0.735 AC: 2551 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.36
CADD	Benign	17
DANN	Benign	0.82
PhyloP100		0.85

Splicing

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

Other links and lift over

dbSNP: rs10033464; hg19: chr4-111720761;