rs1033210

Variant names:

• chr2-147038778-C-T
• rs1033210

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.105 in 152,146 control chromosomes in the GnomAD database, including 1,272 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 0.10 (1272 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.415

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.215 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: 0.104 AC: 15866 AN: 152028 Hom.: 1249 Cov.: 32

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0779

Gnomad ASJ AF: 0.0957

Gnomad EAS AF: 0.107

Gnomad SAS AF: 0.0656

Gnomad FIN AF: 0.0718

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0508

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.105 AC: 15932 AN: 152146 Hom.: 1272 Cov.: 32 AF XY: 0.104 AC XY: 7726 AN XY: 74386

Gnomad4 AFR AF: 0.219

Gnomad4 AMR AF: 0.0777

Gnomad4 ASJ AF: 0.0957

Gnomad4 EAS AF: 0.107

Gnomad4 SAS AF: 0.0657

Gnomad4 FIN AF: 0.0718

Gnomad4 NFE AF: 0.0508

Gnomad4 OTH AF: 0.0993

Alfa AF: 0.0714 Hom.: 137

Bravo AF: 0.113

Asia WGS AF: 0.0980 AC: 342 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.6
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1033210; hg19: chr2-147796346;