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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000560900.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000259754	ENST00000560900.1	TSL:4	n.196-16145G>A		intron	N/A
	ENSG00000287439	ENST00000657831.2		n.441+11073C>T		intron	N/A
	ENSG00000259754	ENST00000662551.1		n.189-16145G>A		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2924566;

hg19: chr15-48268761;