2-150646829-C-T

Variant names:

• chr2-150646829-C-T
• rs10432416

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 0.0614 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0150 AC: 624 AN: 41522

American (AMR) AF: 0.0489 AC: 747 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.109 AC: 380 AN: 3472

East Asian (EAS) AF: 0.122 AC: 632 AN: 5176

South Asian (SAS) AF: 0.0372 AC: 179 AN: 4812

European-Finnish (FIN) AF: 0.0975 AC: 1031 AN: 10572

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0807 AC: 5490 AN: 67998

Other (OTH) AF: 0.0687 AC: 145 AN: 2112

Alfa AF: 0.0664 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
PhyloP100		0.97

Splicing

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

Other links and lift over

dbSNP: rs10432416; hg19: chr2-151503343;