2-150646829-C-T

Variant names:

• chr2-150646829-C-T
• rs10432416

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 0.0614 in 152,156 control chromosomes in the GnomAD database, including 384 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 0.061 (384 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.969

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.114 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: 0.0615 AC: 9356 AN: 152038 Hom.: 385 Cov.: 33

Gnomad AFR AF: 0.0151

Gnomad AMI AF: 0.117

Gnomad AMR AF: 0.0489

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.123

Gnomad SAS AF: 0.0374

Gnomad FIN AF: 0.0975

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0807

Gnomad OTH AF: 0.0679

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

GnomAD4 genome AF: 0.0614 AC: 9349 AN: 152156 Hom.: 384 Cov.: 33 AF XY: 0.0620 AC XY: 4614 AN XY: 74388

Gnomad4 AFR AF: 0.0150

Gnomad4 AMR AF: 0.0489

Gnomad4 ASJ AF: 0.109

Gnomad4 EAS AF: 0.122

Gnomad4 SAS AF: 0.0372

Gnomad4 FIN AF: 0.0975

Gnomad4 NFE AF: 0.0807

Gnomad4 OTH AF: 0.0687

Alfa AF: 0.0683 Hom.: 48

Bravo AF: 0.0575

Asia WGS AF: 0.0510 AC: 178 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	6.3
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10432416; hg19: chr2-151503343;