rs275652

Variant names:

• chr3-148697197-T-G
• rs275652

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 0.195 in 152,100 control chromosomes in the GnomAD database, including 3,147 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 0.19 (3147 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.02
• Publications: 20 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.252 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: 0.195 AC: 29572 AN: 151982 Hom.: 3138 Cov.: 32

Gnomad AFR AF: 0.256

Gnomad AMI AF: 0.258

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.180

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.195 AC: 29607 AN: 152100 Hom.: 3147 Cov.: 32 AF XY: 0.192 AC XY: 14254 AN XY: 74364

African (AFR) AF: 0.256 AC: 10618 AN: 41480

American (AMR) AF: 0.151 AC: 2311 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.282 AC: 978 AN: 3472

East Asian (EAS) AF: 0.118 AC: 612 AN: 5170

South Asian (SAS) AF: 0.126 AC: 606 AN: 4814

European-Finnish (FIN) AF: 0.141 AC: 1489 AN: 10586

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.180 AC: 12247 AN: 67972

Other (OTH) AF: 0.204 AC: 432 AN: 2114

Alfa AF: 0.186 Hom.: 559

Bravo AF: 0.198

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	-0.85
CADD	Benign	6.9
DANN	Benign	0.68
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs275652; hg19: chr3-148414984;