rs965353

Variant names:

• chr15-59768007-G-A
• rs965353

Your query was ambiguous. Multiple possible variants found:

• chr15-59768007-G-A
• chr15-59768007-G-C
• chr15-59768007-G-T

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 0.664 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
• Publications: 5 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.469 AC: 19303 AN: 41188

American (AMR) AF: 0.749 AC: 11411 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.758 AC: 2626 AN: 3466

East Asian (EAS) AF: 0.574 AC: 2956 AN: 5154

South Asian (SAS) AF: 0.691 AC: 3319 AN: 4800

European-Finnish (FIN) AF: 0.685 AC: 7144 AN: 10426

Middle Eastern (MID) AF: 0.743 AC: 217 AN: 292

European-Non Finnish (NFE) AF: 0.760 AC: 51618 AN: 67912

Other (OTH) AF: 0.682 AC: 1427 AN: 2092

Alfa AF: 0.733 Hom.: 21630

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
PhyloP100		-0.017

Splicing

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

Other links and lift over

dbSNP: rs965353; hg19: chr15-60060206;