3-148650554-C-A

Variant names:

• chr3-148650554-C-A
• rs275678

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 0.214 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
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.239 AC: 9892 AN: 41474

American (AMR) AF: 0.167 AC: 2550 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.322 AC: 1116 AN: 3470

East Asian (EAS) AF: 0.129 AC: 665 AN: 5168

South Asian (SAS) AF: 0.193 AC: 929 AN: 4818

European-Finnish (FIN) AF: 0.138 AC: 1463 AN: 10584

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.222 AC: 15075 AN: 67980

Other (OTH) AF: 0.245 AC: 518 AN: 2116

Alfa AF: 0.222 Hom.: 755

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
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs275678; hg19: chr3-148368341;