rs560766

Variant names:

• chr15-34708741-G-A
• rs560766
• ENST00000720751.1:n.234+11576C>T

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. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000720751.1(ENSG00000294065):​n.234+11576C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000294065 ENST00000720751.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.82
• Publications: 13 publications found

Genes affected

ENSG00000294065 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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
ENSG00000294065	ENST00000720751.1	n.234+11576C>T		intron_variant	Intron 1 of 1
ENSG00000294065	ENST00000720752.1	n.188-5199C>T		intron_variant	Intron 1 of 1

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

African (AFR) AF: 0.552 AC: 22863 AN: 41422

American (AMR) AF: 0.399 AC: 6098 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.384 AC: 1330 AN: 3464

East Asian (EAS) AF: 0.437 AC: 2256 AN: 5162

South Asian (SAS) AF: 0.590 AC: 2840 AN: 4816

European-Finnish (FIN) AF: 0.349 AC: 3678 AN: 10548

Middle Eastern (MID) AF: 0.336 AC: 98 AN: 292

European-Non Finnish (NFE) AF: 0.430 AC: 29212 AN: 67940

Other (OTH) AF: 0.450 AC: 949 AN: 2110

Alfa AF: 0.444 Hom.: 9458

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
PhyloP100		1.8

Splicing

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

Other links and lift over

dbSNP: rs560766; hg19: chr15-35000942;