15-26509934-C-G

Variant names:

• chr15-26509934-C-G
• rs1593610
• ENST00000660088.2:n.233+8442G>C

Variant summary

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

The ENST00000660088.2(ENSG00000287280):​n.233+8442G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.409 in 151,956 control chromosomes in the GnomAD database, including 13,035 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 0.41 (13035 hom., cov: 32)
• Consequence: ENSG00000287280 ENST00000660088.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0890
• Publications: 2 publications found

Genes affected

ENSG00000287280 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.482 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000660088.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287280	ENST00000660088.2		n.233+8442G>C		intron	N/A
	ENSG00000287280	ENST00000826682.1		n.198+8442G>C		intron	N/A
	ENSG00000287280	ENST00000826683.1		n.233+8442G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.409 AC: 62098 AN: 151836 Hom.: 13013 Cov.: 32

Gnomad AFR AF: 0.488

Gnomad AMI AF: 0.393

Gnomad AMR AF: 0.371

Gnomad ASJ AF: 0.406

Gnomad EAS AF: 0.319

Gnomad SAS AF: 0.291

Gnomad FIN AF: 0.360

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.394

Gnomad OTH AF: 0.379

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

GnomAD4 genome AF: 0.409 AC: 62155 AN: 151956 Hom.: 13035 Cov.: 32 AF XY: 0.403 AC XY: 29957 AN XY: 74246

African (AFR) AF: 0.488 AC: 20219 AN: 41430

American (AMR) AF: 0.370 AC: 5647 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.406 AC: 1410 AN: 3470

East Asian (EAS) AF: 0.319 AC: 1649 AN: 5166

South Asian (SAS) AF: 0.292 AC: 1407 AN: 4824

European-Finnish (FIN) AF: 0.360 AC: 3803 AN: 10552

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.394 AC: 26760 AN: 67954

Other (OTH) AF: 0.377 AC: 795 AN: 2106

Alfa AF: 0.297 Hom.: 829

Bravo AF: 0.413

Asia WGS AF: 0.316 AC: 1097 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.64
PhyloP100		-0.089

Splicing

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

Other links and lift over

dbSNP: rs1593610; hg19: chr15-26755081;