rs10490996

Positions:

• chr10-78371685-G-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, non coding transcript 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: ENST00000421324.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.18

Genes affected

(HGNC:):

LINC00595 (HGNC:31430): (long intergenic non-protein coding RNA 595)

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000421324.4	n.50+133381G>A		intron_variant, non_coding_transcript_variant		1
LINC00595	ENST00000635422.1	n.63-153645G>A		intron_variant, non_coding_transcript_variant		5

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;