2-148800291-T-C

Variant names:

• chr2-148800291-T-C
• rs2121433

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 0.568 in 152,020 control chromosomes in the GnomAD database, including 27,465 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 0.57 (27465 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.281
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.726 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: 0.568 AC: 86302 AN: 151902 Hom.: 27471 Cov.: 32

Gnomad AFR AF: 0.321

Gnomad AMI AF: 0.678

Gnomad AMR AF: 0.549

Gnomad ASJ AF: 0.708

Gnomad EAS AF: 0.185

Gnomad SAS AF: 0.441

Gnomad FIN AF: 0.691

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.731

Gnomad OTH AF: 0.611

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

GnomAD4 genome AF: 0.568 AC: 86289 AN: 152020 Hom.: 27465 Cov.: 32 AF XY: 0.561 AC XY: 41701 AN XY: 74318

African (AFR) AF: 0.321 AC: 13297 AN: 41464

American (AMR) AF: 0.548 AC: 8368 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.708 AC: 2456 AN: 3470

East Asian (EAS) AF: 0.186 AC: 960 AN: 5174

South Asian (SAS) AF: 0.441 AC: 2127 AN: 4824

European-Finnish (FIN) AF: 0.691 AC: 7285 AN: 10544

Middle Eastern (MID) AF: 0.724 AC: 213 AN: 294

European-Non Finnish (NFE) AF: 0.731 AC: 49687 AN: 67968

Other (OTH) AF: 0.605 AC: 1278 AN: 2112

Alfa AF: 0.674 Hom.: 164852

Bravo AF: 0.545

Asia WGS AF: 0.303 AC: 1056 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	1.1
DANN	Benign	0.83
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs2121433; hg19: chr2-149557860;