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

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

Gnomad4 AFR AF: 0.256 AC: 0.255979 AN: 0.255979

Gnomad4 AMR AF: 0.151 AC: 0.151184 AN: 0.151184

Gnomad4 ASJ AF: 0.282 AC: 0.281682 AN: 0.281682

Gnomad4 EAS AF: 0.118 AC: 0.118375 AN: 0.118375

Gnomad4 SAS AF: 0.126 AC: 0.125883 AN: 0.125883

Gnomad4 FIN AF: 0.141 AC: 0.140657 AN: 0.140657

Gnomad4 NFE AF: 0.180 AC: 0.180177 AN: 0.180177

Gnomad4 OTH AF: 0.204 AC: 0.204352 AN: 0.204352

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs275652; hg19: chr3-148414984;