2-150129251-G-T

Variant names:

• chr2-150129251-G-T
• rs330609

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 0.439 in 151,942 control chromosomes in the GnomAD database, including 16,284 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 0.44 (16284 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.125
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.656 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: 0.439 AC: 66650 AN: 151824 Hom.: 16276 Cov.: 32

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.449

Gnomad AMR AF: 0.514

Gnomad ASJ AF: 0.448

Gnomad EAS AF: 0.675

Gnomad SAS AF: 0.526

Gnomad FIN AF: 0.540

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.518

Gnomad OTH AF: 0.431

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

GnomAD4 genome AF: 0.439 AC: 66660 AN: 151942 Hom.: 16284 Cov.: 32 AF XY: 0.443 AC XY: 32888 AN XY: 74220

African (AFR) AF: 0.214 AC: 8880 AN: 41432

American (AMR) AF: 0.515 AC: 7868 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.448 AC: 1555 AN: 3470

East Asian (EAS) AF: 0.675 AC: 3477 AN: 5150

South Asian (SAS) AF: 0.525 AC: 2526 AN: 4812

European-Finnish (FIN) AF: 0.540 AC: 5696 AN: 10544

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.518 AC: 35223 AN: 67950

Other (OTH) AF: 0.427 AC: 903 AN: 2114

Alfa AF: 0.489 Hom.: 63457

Bravo AF: 0.430

Asia WGS AF: 0.510 AC: 1770 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.96
DANN	Benign	0.38
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs330609; hg19: chr2-150985765;