3-148662756-C-T

Variant names:

• chr3-148662756-C-T
• rs718424

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 0.516 in 151,698 control chromosomes in the GnomAD database, including 23,166 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 0.52 (23166 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.597
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.79 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: 0.516 AC: 78282 AN: 151582 Hom.: 23152 Cov.: 32

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.533

Gnomad AMR AF: 0.676

Gnomad ASJ AF: 0.545

Gnomad EAS AF: 0.810

Gnomad SAS AF: 0.539

Gnomad FIN AF: 0.675

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.616

Gnomad OTH AF: 0.529

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

GnomAD4 genome AF: 0.516 AC: 78318 AN: 151698 Hom.: 23166 Cov.: 32 AF XY: 0.523 AC XY: 38757 AN XY: 74122

African (AFR) AF: 0.211 AC: 8733 AN: 41390

American (AMR) AF: 0.677 AC: 10281 AN: 15196

Ashkenazi Jewish (ASJ) AF: 0.545 AC: 1887 AN: 3460

East Asian (EAS) AF: 0.810 AC: 4180 AN: 5158

South Asian (SAS) AF: 0.541 AC: 2607 AN: 4818

European-Finnish (FIN) AF: 0.675 AC: 7112 AN: 10538

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.616 AC: 41787 AN: 67832

Other (OTH) AF: 0.529 AC: 1113 AN: 2102

Alfa AF: 0.586 Hom.: 14307

Bravo AF: 0.509

Asia WGS AF: 0.630 AC: 2176 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	9.3
DANN	Benign	0.24
PhyloP100		0.60

Splicing

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

Other links and lift over

dbSNP: rs718424; hg19: chr3-148380543;