rs10042486

Variant names:

• chr5-63965502-C-T
• rs10042486
• ENST00000502882.1:n.97-7487G>A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The ENST00000502882.1(ENSG00000248285):​n.97-7487G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.576 in 151,620 control chromosomes in the GnomAD database, including 26,145 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.58 (26145 hom., cov: 31)
• Consequence: ENSG00000248285 ENST00000502882.1 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.484

Genes affected

ENSG00000248285 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BP6: Variant 5-63965502-C-T is Benign according to our data. Variant chr5-63965502-C-T is described in ClinVar as [Benign]. Clinvar id is 1252728.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.772 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000248285	ENST00000502882.1	n.97-7487G>A		intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes AF: 0.576 AC: 87204 AN: 151504 Hom.: 26104 Cov.: 31

Gnomad AFR AF: 0.727

Gnomad AMI AF: 0.700

Gnomad AMR AF: 0.520

Gnomad ASJ AF: 0.535

Gnomad EAS AF: 0.792

Gnomad SAS AF: 0.591

Gnomad FIN AF: 0.428

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.501

Gnomad OTH AF: 0.571

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

GnomAD4 genome AF: 0.576 AC: 87291 AN: 151620 Hom.: 26145 Cov.: 31 AF XY: 0.573 AC XY: 42469 AN XY: 74086

Gnomad4 AFR AF: 0.728

Gnomad4 AMR AF: 0.520

Gnomad4 ASJ AF: 0.535

Gnomad4 EAS AF: 0.792

Gnomad4 SAS AF: 0.589

Gnomad4 FIN AF: 0.428

Gnomad4 NFE AF: 0.501

Gnomad4 OTH AF: 0.572

Alfa AF: 0.517 Hom.: 21554

Bravo AF: 0.589

Asia WGS AF: 0.667 AC: 2318 AN: 3474

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Mar 09, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10042486; hg19: chr5-63261329;