rs2924566

Variant names:

• chr15-47976564-G-A
• rs2924566
• ENST00000560900.1:n.196-16145G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000560900.1(ENSG00000259754):​n.196-16145G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.611 in 152,024 control chromosomes in the GnomAD database, including 32,473 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 0.61 (32473 hom., cov: 32)
• Consequence: ENSG00000259754 ENST00000560900.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0600
• Publications: 2 publications found

Genes affected

ENSG00000259754 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.796 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124900354	XR_001751516.3	n.143-16145G>A		intron_variant	Intron 1 of 2
LOC124900354	XR_001751517.2	n.143-16145G>A		intron_variant	Intron 1 of 2
LOC124900354	XR_001751518.3	n.83-16145G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000259754	ENST00000560900.1	n.196-16145G>A		intron_variant	Intron 1 of 2	4
ENSG00000287439	ENST00000657831.2	n.441+11073C>T		intron_variant	Intron 1 of 2
ENSG00000259754	ENST00000662551.1	n.189-16145G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.611 AC: 92857 AN: 151906 Hom.: 32486 Cov.: 32

Gnomad AFR AF: 0.305

Gnomad AMI AF: 0.784

Gnomad AMR AF: 0.569

Gnomad ASJ AF: 0.761

Gnomad EAS AF: 0.175

Gnomad SAS AF: 0.626

Gnomad FIN AF: 0.783

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.801

Gnomad OTH AF: 0.629

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

GnomAD4 genome AF: 0.611 AC: 92847 AN: 152024 Hom.: 32473 Cov.: 32 AF XY: 0.610 AC XY: 45290 AN XY: 74304

African (AFR) AF: 0.304 AC: 12607 AN: 41444

American (AMR) AF: 0.568 AC: 8682 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.761 AC: 2642 AN: 3472

East Asian (EAS) AF: 0.175 AC: 904 AN: 5160

South Asian (SAS) AF: 0.627 AC: 3009 AN: 4802

European-Finnish (FIN) AF: 0.783 AC: 8276 AN: 10576

Middle Eastern (MID) AF: 0.793 AC: 233 AN: 294

European-Non Finnish (NFE) AF: 0.801 AC: 54461 AN: 67970

Other (OTH) AF: 0.624 AC: 1320 AN: 2114

Alfa AF: 0.664 Hom.: 6346

Bravo AF: 0.576

Asia WGS AF: 0.362 AC: 1259 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.0
DANN	Benign	0.78
PhyloP100		0.060

Splicing

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

Other links and lift over

dbSNP: rs2924566; hg19: chr15-48268761;