rs13069049

Positions:

• chr3-66759518-A-T

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 152,182 control chromosomes in the GnomAD database, including 1,887 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 (1887 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.419

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 = 0.183 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.151 AC: 22946 AN: 152064 Hom.: 1887 Cov.: 32

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.0735

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.143

Gnomad EAS AF: 0.165

Gnomad SAS AF: 0.0947

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.151 AC: 22966 AN: 152182 Hom.: 1887 Cov.: 32 AF XY: 0.149 AC XY: 11063 AN XY: 74408

Gnomad4 AFR AF: 0.107

Gnomad4 AMR AF: 0.150

Gnomad4 ASJ AF: 0.143

Gnomad4 EAS AF: 0.165

Gnomad4 SAS AF: 0.0942

Gnomad4 FIN AF: 0.136

Gnomad4 NFE AF: 0.185

Gnomad4 OTH AF: 0.137

Alfa AF: 0.159 Hom.: 235

Bravo AF: 0.150

Asia WGS AF: 0.127 AC: 441 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	4.3
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13069049; hg19: chr3-66809942;