17-14517259-A-G

Variant names:

• chr17-14517259-A-G
• rs2323287
• ENST00000700765.2:n.439-8926A>G

Variant summary

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

The ENST00000700765.2(ENSG00000230647):​n.439-8926A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.891 in 152,170 control chromosomes in the GnomAD database, including 61,607 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 0.89 (61607 hom., cov: 32)
• Consequence: ENSG00000230647 ENST00000700765.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.108
• Publications: 0 publications found

Genes affected

ENSG00000230647 (HGNC:58488):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.988 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000700765.2. 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
	ENSG00000230647	ENST00000700765.2		n.439-8926A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.891 AC: 135479 AN: 152052 Hom.: 61618 Cov.: 32

Gnomad AFR AF: 0.729

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.890

Gnomad ASJ AF: 0.976

Gnomad EAS AF: 0.560

Gnomad SAS AF: 0.935

Gnomad FIN AF: 0.963

Gnomad MID AF: 0.940

Gnomad NFE AF: 0.994

Gnomad OTH AF: 0.906

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

GnomAD4 genome AF: 0.891 AC: 135510 AN: 152170 Hom.: 61607 Cov.: 32 AF XY: 0.889 AC XY: 66099 AN XY: 74388

African (AFR) AF: 0.728 AC: 30198 AN: 41470

American (AMR) AF: 0.889 AC: 13583 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.976 AC: 3388 AN: 3472

East Asian (EAS) AF: 0.560 AC: 2888 AN: 5160

South Asian (SAS) AF: 0.935 AC: 4508 AN: 4820

European-Finnish (FIN) AF: 0.963 AC: 10231 AN: 10624

Middle Eastern (MID) AF: 0.942 AC: 277 AN: 294

European-Non Finnish (NFE) AF: 0.994 AC: 67616 AN: 68026

Other (OTH) AF: 0.903 AC: 1909 AN: 2114

Alfa AF: 0.933 Hom.: 8669

Bravo AF: 0.877

Asia WGS AF: 0.752 AC: 2616 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.0
DANN	Benign	0.78
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs2323287; hg19: chr17-14420576;