17-14517259-A-G

Position:

• chr17-14517259-A-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, non coding transcript 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: ENST00000700765.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.108

Genes affected

(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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000700765.1	n.421-8926A>G		intron_variant, non_coding_transcript_variant

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;