ENST00000560900.1:n.258+26442A>C

Variant names:

• chr15-48019213-A-C
• rs9788730
• ENST00000560900.1:n.258+26442A>C

Variant summary

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

The ENST00000560900.1(ENSG00000259754):​n.258+26442A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.266 in 152,050 control chromosomes in the GnomAD database, including 9,868 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 0.27 (9868 hom., cov: 33)
• Consequence: ENSG00000259754 ENST00000560900.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0720
• Publications: 0 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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.804 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124900354	XR_001751516.3	n.205+26442A>C		intron_variant	Intron 2 of 2
LOC124900354	XR_001751518.3	n.145+26442A>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000259754	ENST00000560900.1	n.258+26442A>C		intron_variant	Intron 2 of 2	4
ENSG00000259754	ENST00000662551.1	n.251+26442A>C		intron_variant	Intron 2 of 2
ENSG00000259754	ENST00000665188.1	n.220+21058A>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.265 AC: 40320 AN: 151930 Hom.: 9827 Cov.: 33

Gnomad AFR AF: 0.574

Gnomad AMI AF: 0.0252

Gnomad AMR AF: 0.283

Gnomad ASJ AF: 0.0963

Gnomad EAS AF: 0.825

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.0546

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.0821

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.266 AC: 40429 AN: 152050 Hom.: 9868 Cov.: 33 AF XY: 0.265 AC XY: 19678 AN XY: 74336

African (AFR) AF: 0.574 AC: 23776 AN: 41406

American (AMR) AF: 0.283 AC: 4329 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0963 AC: 334 AN: 3468

East Asian (EAS) AF: 0.824 AC: 4269 AN: 5178

South Asian (SAS) AF: 0.203 AC: 975 AN: 4810

European-Finnish (FIN) AF: 0.0546 AC: 580 AN: 10614

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.0821 AC: 5581 AN: 67990

Other (OTH) AF: 0.250 AC: 526 AN: 2106

Alfa AF: 0.144 Hom.: 5272

Bravo AF: 0.303

Asia WGS AF: 0.539 AC: 1873 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.0
DANN	Benign	0.78
PhyloP100		0.072

Splicing

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

Other links and lift over

dbSNP: rs9788730; hg19: chr15-48311410;