3-66748526-C-G

Variant names:

• chr3-66748526-C-G
• rs13069000

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 0.151 in 152,060 control chromosomes in the GnomAD database, including 1,895 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 0.15 (1895 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.112

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.184 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: 0.151 AC: 22968 AN: 151942 Hom.: 1895 Cov.: 32

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.0735

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.165

Gnomad SAS AF: 0.0952

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.135

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

GnomAD4 genome AF: 0.151 AC: 22980 AN: 152060 Hom.: 1895 Cov.: 32 AF XY: 0.149 AC XY: 11045 AN XY: 74334

Gnomad4 AFR AF: 0.107

Gnomad4 AMR AF: 0.149

Gnomad4 ASJ AF: 0.144

Gnomad4 EAS AF: 0.165

Gnomad4 SAS AF: 0.0946

Gnomad4 FIN AF: 0.136

Gnomad4 NFE AF: 0.186

Gnomad4 OTH AF: 0.136

Alfa AF: 0.180 Hom.: 1403

Bravo AF: 0.150

Asia WGS AF: 0.126 AC: 438 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.2
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13069000; hg19: chr3-66798950;