2-10946024-T-C

Position:

• chr2-10946024-T-C

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 0.548 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.343

Gnomad4 AMR AF: 0.616

Gnomad4 ASJ AF: 0.601

Gnomad4 EAS AF: 0.631

Gnomad4 SAS AF: 0.464

Gnomad4 FIN AF: 0.642

Gnomad4 NFE AF: 0.638

Gnomad4 OTH AF: 0.528

Alfa AF: 0.610 Hom.: 15198

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2003298; hg19: chr2-11086150;