3-66759518-A-T

Variant names:

• chr3-66759518-A-T
• rs13069049

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 0.151 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
• Publications: 10 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.107 AC: 4445 AN: 41508

American (AMR) AF: 0.150 AC: 2295 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.143 AC: 496 AN: 3466

East Asian (EAS) AF: 0.165 AC: 855 AN: 5180

South Asian (SAS) AF: 0.0942 AC: 454 AN: 4820

European-Finnish (FIN) AF: 0.136 AC: 1441 AN: 10596

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.185 AC: 12601 AN: 68006

Other (OTH) AF: 0.137 AC: 290 AN: 2116

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
PhyloP100		0.42

Splicing

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

Other links and lift over

dbSNP: rs13069049; hg19: chr3-66809942;