3-148689012-G-T

Variant names:

• chr3-148689012-G-T
• rs2933251

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 0.2 in 151,918 control chromosomes in the GnomAD database, including 3,379 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 0.20 (3379 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.108
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.271 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: 0.200 AC: 30422 AN: 151800 Hom.: 3370 Cov.: 32

Gnomad AFR AF: 0.275

Gnomad AMI AF: 0.258

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.287

Gnomad EAS AF: 0.119

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.264

Gnomad NFE AF: 0.181

Gnomad OTH AF: 0.209

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

GnomAD4 genome AF: 0.200 AC: 30455 AN: 151918 Hom.: 3379 Cov.: 32 AF XY: 0.198 AC XY: 14665 AN XY: 74244

African (AFR) AF: 0.275 AC: 11385 AN: 41380

American (AMR) AF: 0.153 AC: 2332 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.287 AC: 997 AN: 3470

East Asian (EAS) AF: 0.119 AC: 614 AN: 5164

South Asian (SAS) AF: 0.126 AC: 605 AN: 4814

European-Finnish (FIN) AF: 0.141 AC: 1495 AN: 10572

Middle Eastern (MID) AF: 0.267 AC: 78 AN: 292

European-Non Finnish (NFE) AF: 0.181 AC: 12278 AN: 67954

Other (OTH) AF: 0.207 AC: 436 AN: 2108

Alfa AF: 0.0953 Hom.: 186

Bravo AF: 0.204

Asia WGS AF: 0.131 AC: 461 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.9
DANN	Benign	0.83
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs2933251; hg19: chr3-148406799;