rs17716275

Positions:

• chr19-29086323-G-A

Variant summary

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

The ENST00000656834.1(ENSG00000288017):​n.139-1757C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0637 in 152,198 control chromosomes in the GnomAD database, including 387 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 0.064 (387 hom., cov: 33)
• Consequence: ENSG00000288017 ENST00000656834.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.596

Genes affected

ENSG00000288017 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.145 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124904682	XR_007067213.1	n.159-1757C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000288017	ENST00000656834.1	n.139-1757C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.0636 AC: 9676 AN: 152082 Hom.: 386 Cov.: 33

Gnomad AFR AF: 0.0793

Gnomad AMI AF: 0.0804

Gnomad AMR AF: 0.0499

Gnomad ASJ AF: 0.0349

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.0364

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0491

Gnomad OTH AF: 0.0645

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

GnomAD4 genome AF: 0.0637 AC: 9690 AN: 152198 Hom.: 387 Cov.: 33 AF XY: 0.0657 AC XY: 4891 AN XY: 74408

Gnomad4 AFR AF: 0.0793

Gnomad4 AMR AF: 0.0499

Gnomad4 ASJ AF: 0.0349

Gnomad4 EAS AF: 0.153

Gnomad4 SAS AF: 0.154

Gnomad4 FIN AF: 0.0364

Gnomad4 NFE AF: 0.0491

Gnomad4 OTH AF: 0.0681

Alfa AF: 0.0525 Hom.: 125

Bravo AF: 0.0642

Asia WGS AF: 0.158 AC: 553 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.7
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17716275; hg19: chr19-29577230;