rs965353

chr15-59768007-G-Achr15-59768007-G-Cchr15-59768007-G-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 0.664 in 151,476 control chromosomes in the GnomAD database, including 34,704 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 0.66 (34704 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0170

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.755 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: 0.665 AC: 100617 AN: 151358 Hom.: 34700 Cov.: 30

Gnomad AFR AF: 0.469

Gnomad AMI AF: 0.693

Gnomad AMR AF: 0.749

Gnomad ASJ AF: 0.758

Gnomad EAS AF: 0.573

Gnomad SAS AF: 0.691

Gnomad FIN AF: 0.685

Gnomad MID AF: 0.742

Gnomad NFE AF: 0.760

Gnomad OTH AF: 0.686

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

GnomAD4 genome AF: 0.664 AC: 100652 AN: 151476 Hom.: 34704 Cov.: 30 AF XY: 0.664 AC XY: 49135 AN XY: 73976

Gnomad4 AFR AF: 0.469

Gnomad4 AMR AF: 0.749

Gnomad4 ASJ AF: 0.758

Gnomad4 EAS AF: 0.574

Gnomad4 SAS AF: 0.691

Gnomad4 FIN AF: 0.685

Gnomad4 NFE AF: 0.760

Gnomad4 OTH AF: 0.682

Alfa AF: 0.730 Hom.: 14547

Bravo AF: 0.657

Asia WGS AF: 0.643 AC: 2228 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
Cadd	Benign	2.3
Dann	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs965353; hg19: chr15-60060206;