17-47072043-C-T

Position:

• chr17-47072043-C-T

Variant summary

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

The ENST00000668245.1(ENSG00000262879):​n.36-15290G>A 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 0.454 in 151,824 control chromosomes in the GnomAD database, including 16,223 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 0.45 (16223 hom., cov: 30)
• Consequence: ENST00000668245.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.103

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.512 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101927060	XR_007065805.1	n.539+429G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000668245.1	n.36-15290G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.454 AC: 68861 AN: 151708 Hom.: 16211 Cov.: 30

Gnomad AFR AF: 0.340

Gnomad AMI AF: 0.479

Gnomad AMR AF: 0.461

Gnomad ASJ AF: 0.625

Gnomad EAS AF: 0.265

Gnomad SAS AF: 0.488

Gnomad FIN AF: 0.507

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.517

Gnomad OTH AF: 0.438

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

GnomAD4 genome AF: 0.454 AC: 68898 AN: 151824 Hom.: 16223 Cov.: 30 AF XY: 0.454 AC XY: 33725 AN XY: 74220

Gnomad4 AFR AF: 0.340

Gnomad4 AMR AF: 0.461

Gnomad4 ASJ AF: 0.625

Gnomad4 EAS AF: 0.265

Gnomad4 SAS AF: 0.489

Gnomad4 FIN AF: 0.507

Gnomad4 NFE AF: 0.517

Gnomad4 OTH AF: 0.439

Alfa AF: 0.363 Hom.: 1023

Bravo AF: 0.444

Asia WGS AF: 0.413 AC: 1434 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.1
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4074249; hg19: chr17-45149409;