rs10490996

Variant names:

• chr10-78371685-G-A
• rs10490996
• ENST00000421324.4:n.50+133381G>A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000421324.4(ENSG00000282863):​n.50+133381G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.091 in 152,182 control chromosomes in the GnomAD database, including 629 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 0.091 (629 hom., cov: 33)
• Consequence: ENSG00000282863 ENST00000421324.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.18

Genes affected

ENSG00000282863 (HGNC:):

LINC00595 (HGNC:45111): (long intergenic non-protein coding RNA 856)

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.26).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.112 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
ENSG00000282863	ENST00000421324.4	n.50+133381G>A		intron_variant	Intron 1 of 2	1
LINC00595	ENST00000624665.3	n.331+122615G>A		intron_variant	Intron 1 of 3	2
LINC00595	ENST00000634389.1	n.408-24726G>A		intron_variant	Intron 3 of 3	4

Frequencies

GnomAD3 genomes AF: 0.0910 AC: 13831 AN: 152064 Hom.: 625 Cov.: 33

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.0515

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.0401

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.0808

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0819

Gnomad OTH AF: 0.0886

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

GnomAD4 genome AF: 0.0910 AC: 13848 AN: 152182 Hom.: 629 Cov.: 33 AF XY: 0.0932 AC XY: 6934 AN XY: 74396

Gnomad4 AFR AF: 0.101

Gnomad4 AMR AF: 0.116

Gnomad4 ASJ AF: 0.144

Gnomad4 EAS AF: 0.0400

Gnomad4 SAS AF: 0.104

Gnomad4 FIN AF: 0.0808

Gnomad4 NFE AF: 0.0819

Gnomad4 OTH AF: 0.0872

Alfa AF: 0.0879 Hom.: 877

Bravo AF: 0.0910

Asia WGS AF: 0.0520 AC: 182 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.26
CADD	Benign	21
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10490996; hg19: chr10-80131442;