rs1033210

Positions:

• chr2-147038778-C-T

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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.415

Genes affected

(HGNC:):

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/exons	MANE	Protein	UniProt
		n.147038778C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;