rs13066695

chr3-127101845-T-C

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 0.411 in 150,772 control chromosomes in the GnomAD database, including 13,075 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 0.41 (13075 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.295

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.547 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: 0.410 AC: 61834 AN: 150652 Hom.: 13053 Cov.: 30

Gnomad AFR AF: 0.515

Gnomad AMI AF: 0.305

Gnomad AMR AF: 0.301

Gnomad ASJ AF: 0.360

Gnomad EAS AF: 0.564

Gnomad SAS AF: 0.499

Gnomad FIN AF: 0.414

Gnomad MID AF: 0.306

Gnomad NFE AF: 0.359

Gnomad OTH AF: 0.375

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

GnomAD4 genome AF: 0.411 AC: 61909 AN: 150772 Hom.: 13075 Cov.: 30 AF XY: 0.415 AC XY: 30558 AN XY: 73664

Gnomad4 AFR AF: 0.515

Gnomad4 AMR AF: 0.301

Gnomad4 ASJ AF: 0.360

Gnomad4 EAS AF: 0.564

Gnomad4 SAS AF: 0.500

Gnomad4 FIN AF: 0.414

Gnomad4 NFE AF: 0.359

Gnomad4 OTH AF: 0.379

Alfa AF: 0.361 Hom.: 14957

Bravo AF: 0.402

Asia WGS AF: 0.560 AC: 1944 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.28
Dann	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13066695; hg19: chr3-126820688;