rs10033464

Positions:

• chr4-110799605-T-G

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;