rs275678

Positions:

• chr3-148650554-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.214 in 152,096 control chromosomes in the GnomAD database, including 3,631 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 0.21 (3631 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.235 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.214 AC: 32584 AN: 151978 Hom.: 3626 Cov.: 32

Gnomad AFR AF: 0.238

Gnomad AMI AF: 0.332

Gnomad AMR AF: 0.167

Gnomad ASJ AF: 0.322

Gnomad EAS AF: 0.128

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.222

Gnomad OTH AF: 0.246

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

GnomAD4 genome AF: 0.214 AC: 32615 AN: 152096 Hom.: 3631 Cov.: 32 AF XY: 0.211 AC XY: 15670 AN XY: 74368

Gnomad4 AFR AF: 0.239

Gnomad4 AMR AF: 0.167

Gnomad4 ASJ AF: 0.322

Gnomad4 EAS AF: 0.129

Gnomad4 SAS AF: 0.193

Gnomad4 FIN AF: 0.138

Gnomad4 NFE AF: 0.222

Gnomad4 OTH AF: 0.245

Alfa AF: 0.221 Hom.: 726

Bravo AF: 0.215

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.30
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs275678; hg19: chr3-148368341;