rs10491085

Positions:

• chr17-5783253-C-T

Variant summary

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

The ENST00000573619.1(ENSG00000285471):​c.-524+10226C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.783 in 152,056 control chromosomes in the GnomAD database, including 47,993 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 0.78 (47993 hom., cov: 30)
• Consequence: ENSG00000285471 ENST00000573619.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.69

Genes affected

ENSG00000285471 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.873 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC339166	NR_040000.1	n.794+10226C>T		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285471	ENST00000573619.1	c.-524+10226C>T		intron_variant	Intron 1 of 4	2		ENSP00000461865.1
ENSG00000284837	ENST00000563763.5	n.794+10226C>T		intron_variant	Intron 1 of 3	1

Frequencies

GnomAD3 genomes AF: 0.783 AC: 118977 AN: 151938 Hom.: 47960 Cov.: 30

Gnomad AFR AF: 0.666

Gnomad AMI AF: 0.942

Gnomad AMR AF: 0.833

Gnomad ASJ AF: 0.775

Gnomad EAS AF: 0.330

Gnomad SAS AF: 0.522

Gnomad FIN AF: 0.883

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.879

Gnomad OTH AF: 0.791

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

GnomAD4 genome AF: 0.783 AC: 119058 AN: 152056 Hom.: 47993 Cov.: 30 AF XY: 0.774 AC XY: 57547 AN XY: 74318

Gnomad4 AFR AF: 0.665

Gnomad4 AMR AF: 0.833

Gnomad4 ASJ AF: 0.775

Gnomad4 EAS AF: 0.329

Gnomad4 SAS AF: 0.524

Gnomad4 FIN AF: 0.883

Gnomad4 NFE AF: 0.879

Gnomad4 OTH AF: 0.791

Alfa AF: 0.847 Hom.: 90013

Bravo AF: 0.774

Asia WGS AF: 0.488 AC: 1699 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.35
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10491085; hg19: chr17-5686573;