2-10946024-T-C

Variant names:

• chr2-10946024-T-C
• rs2003298

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.548 in 152,232 control chromosomes in the GnomAD database, including 24,077 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 0.55 (24077 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.634
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.633 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: 0.548 AC: 83346 AN: 152114 Hom.: 24072 Cov.: 34

Gnomad AFR AF: 0.343

Gnomad AMI AF: 0.726

Gnomad AMR AF: 0.616

Gnomad ASJ AF: 0.601

Gnomad EAS AF: 0.631

Gnomad SAS AF: 0.465

Gnomad FIN AF: 0.642

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.638

Gnomad OTH AF: 0.532

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

GnomAD4 genome AF: 0.548 AC: 83387 AN: 152232 Hom.: 24077 Cov.: 34 AF XY: 0.548 AC XY: 40823 AN XY: 74434

African (AFR) AF: 0.343 AC: 14250 AN: 41522

American (AMR) AF: 0.616 AC: 9426 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.601 AC: 2085 AN: 3472

East Asian (EAS) AF: 0.631 AC: 3270 AN: 5180

South Asian (SAS) AF: 0.464 AC: 2240 AN: 4826

European-Finnish (FIN) AF: 0.642 AC: 6802 AN: 10600

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.638 AC: 43405 AN: 68016

Other (OTH) AF: 0.528 AC: 1117 AN: 2114

Alfa AF: 0.612 Hom.: 20794

Bravo AF: 0.539

Asia WGS AF: 0.518 AC: 1802 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.2
DANN	Benign	0.58
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs2003298; hg19: chr2-11086150;