17-15289739-A-G

Position:

• chr17-15289739-A-G

Variant summary

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

The ENST00000654786.1(ENSG00000286792):​n.138-17922A>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 0.747 in 152,220 control chromosomes in the GnomAD database, including 42,928 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 0.75 (42928 hom., cov: 34)
• Consequence: ENST00000654786.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.554

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.86 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124903932	XR_007065633.1	n.297+180A>G		intron_variant, non_coding_transcript_variant
LOC124903932	XR_007065634.1	n.297+180A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000654786.1	n.138-17922A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.747 AC: 113579 AN: 152102 Hom.: 42876 Cov.: 34

Gnomad AFR AF: 0.867

Gnomad AMI AF: 0.698

Gnomad AMR AF: 0.714

Gnomad ASJ AF: 0.673

Gnomad EAS AF: 0.810

Gnomad SAS AF: 0.777

Gnomad FIN AF: 0.708

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.684

Gnomad OTH AF: 0.746

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

GnomAD4 genome AF: 0.747 AC: 113687 AN: 152220 Hom.: 42928 Cov.: 34 AF XY: 0.748 AC XY: 55636 AN XY: 74404

Gnomad4 AFR AF: 0.867

Gnomad4 AMR AF: 0.714

Gnomad4 ASJ AF: 0.673

Gnomad4 EAS AF: 0.810

Gnomad4 SAS AF: 0.775

Gnomad4 FIN AF: 0.708

Gnomad4 NFE AF: 0.684

Gnomad4 OTH AF: 0.748

Alfa AF: 0.705 Hom.: 7716

Bravo AF: 0.751

Asia WGS AF: 0.796 AC: 2770 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.7
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1380181; hg19: chr17-15193056; COSMIC: COSV60076220;