rs10033464

Variant names:

• chr4-110799605-T-G
• rs10033464

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.819

Gnomad4 AMR AF: 0.817

Gnomad4 ASJ AF: 0.925

Gnomad4 EAS AF: 0.773

Gnomad4 SAS AF: 0.782

Gnomad4 FIN AF: 0.832

Gnomad4 NFE AF: 0.904

Gnomad4 OTH AF: 0.872

Alfa AF: 0.898 Hom.: 100146

Bravo AF: 0.859

Asia WGS AF: 0.735 AC: 2551 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10033464; hg19: chr4-111720761;