rs560766

Variant names:

• chr15-34708741-G-A
• rs560766

Your query was ambiguous. Multiple possible variants found:

• chr15-34708741-G-A
• chr15-34708741-G-C
• chr15-34708741-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 0.46 in 151,960 control chromosomes in the GnomAD database, including 16,456 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 0.46 (16456 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.82

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 (SAS) allele frequency at 95% confidence interval = 0.572 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: 0.460 AC: 69892 AN: 151842 Hom.: 16428 Cov.: 32

Gnomad AFR AF: 0.551

Gnomad AMI AF: 0.708

Gnomad AMR AF: 0.399

Gnomad ASJ AF: 0.384

Gnomad EAS AF: 0.437

Gnomad SAS AF: 0.591

Gnomad FIN AF: 0.349

Gnomad MID AF: 0.341

Gnomad NFE AF: 0.430

Gnomad OTH AF: 0.449

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

GnomAD4 genome AF: 0.460 AC: 69968 AN: 151960 Hom.: 16456 Cov.: 32 AF XY: 0.457 AC XY: 33959 AN XY: 74274

Gnomad4 AFR AF: 0.552

Gnomad4 AMR AF: 0.399

Gnomad4 ASJ AF: 0.384

Gnomad4 EAS AF: 0.437

Gnomad4 SAS AF: 0.590

Gnomad4 FIN AF: 0.349

Gnomad4 NFE AF: 0.430

Gnomad4 OTH AF: 0.450

Alfa AF: 0.444 Hom.: 8640

Bravo AF: 0.465

Asia WGS AF: 0.536 AC: 1866 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	9.3
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: rs560766; hg19: chr15-35000942;