rs10042486

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 41 publications found

Genes affected

ENSG00000248285 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 VariationId 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000502882.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000248285	ENST00000502882.1	TSL:2	n.97-7487G>A		intron	N/A

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

African (AFR) AF: 0.728 AC: 30144 AN: 41428

American (AMR) AF: 0.520 AC: 7925 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.535 AC: 1854 AN: 3468

East Asian (EAS) AF: 0.792 AC: 4092 AN: 5164

South Asian (SAS) AF: 0.589 AC: 2826 AN: 4796

European-Finnish (FIN) AF: 0.428 AC: 4492 AN: 10494

Middle Eastern (MID) AF: 0.663 AC: 195 AN: 294

European-Non Finnish (NFE) AF: 0.501 AC: 33922 AN: 67732

Other (OTH) AF: 0.572 AC: 1204 AN: 2104

Alfa AF: 0.533 Hom.: 62171

Bravo AF: 0.589

Asia WGS AF: 0.667 AC: 2318 AN: 3474

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.45
PhyloP100		-0.48

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10042486;

hg19: chr5-63261329;