17-14517259-A-G

Variant names:

• chr17-14517259-A-G
• rs2323287
• ENST00000700765.1:n.421-8926A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000700765.1(ENSG00000230647):​n.421-8926A>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 ENST00000700765.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.108

Genes affected

ENSG00000230647 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000230647	ENST00000700765.1	n.421-8926A>G		intron_variant	Intron 3 of 3

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

Gnomad4 AFR AF: 0.728

Gnomad4 AMR AF: 0.889

Gnomad4 ASJ AF: 0.976

Gnomad4 EAS AF: 0.560

Gnomad4 SAS AF: 0.935

Gnomad4 FIN AF: 0.963

Gnomad4 NFE AF: 0.994

Gnomad4 OTH AF: 0.903

Alfa AF: 0.940 Hom.: 8441

Bravo AF: 0.877

Asia WGS AF: 0.752 AC: 2616 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2323287; hg19: chr17-14420576;