2-146614456-C-T

Variant names:

• chr2-146614456-C-T
• rs10928302

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 0.1 in 151,012 control chromosomes in the GnomAD database, including 1,157 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 (1157 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.388
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.192 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: 0.0999 AC: 15069 AN: 150894 Hom.: 1146 Cov.: 32

Gnomad AFR AF: 0.180

Gnomad AMI AF: 0.00220

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.0415

Gnomad EAS AF: 0.202

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.0222

Gnomad MID AF: 0.105

Gnomad NFE AF: 0.0444

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.100 AC: 15110 AN: 151012 Hom.: 1157 Cov.: 32 AF XY: 0.102 AC XY: 7559 AN XY: 73822

African (AFR) AF: 0.181 AC: 7468 AN: 41336

American (AMR) AF: 0.135 AC: 2032 AN: 15098

Ashkenazi Jewish (ASJ) AF: 0.0415 AC: 143 AN: 3446

East Asian (EAS) AF: 0.202 AC: 1035 AN: 5112

South Asian (SAS) AF: 0.200 AC: 962 AN: 4816

European-Finnish (FIN) AF: 0.0222 AC: 234 AN: 10560

Middle Eastern (MID) AF: 0.113 AC: 33 AN: 292

European-Non Finnish (NFE) AF: 0.0444 AC: 2992 AN: 67342

Other (OTH) AF: 0.0995 AC: 209 AN: 2100

Alfa AF: 0.0722 Hom.: 867

Bravo AF: 0.110

Asia WGS AF: 0.183 AC: 636 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	1.7
DANN	Benign	0.52
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs10928302; hg19: chr2-147372024;