rs10490996

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000421324.4(LINC00595):​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: LINC00595 ENST00000421324.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.18
• Publications: 4 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000421324.4. 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
	LINC00595	ENST00000421324.4	TSL:1	n.50+133381G>A		intron	N/A
	LINC00595	ENST00000624665.3	TSL:2	n.331+122615G>A		intron	N/A
	LINC00595	ENST00000634389.1	TSL:4	n.408-24726G>A		intron	N/A

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

African (AFR) AF: 0.101 AC: 4178 AN: 41500

American (AMR) AF: 0.116 AC: 1775 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.144 AC: 500 AN: 3470

East Asian (EAS) AF: 0.0400 AC: 207 AN: 5180

South Asian (SAS) AF: 0.104 AC: 501 AN: 4816

European-Finnish (FIN) AF: 0.0808 AC: 856 AN: 10596

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.0819 AC: 5570 AN: 68004

Other (OTH) AF: 0.0872 AC: 184 AN: 2110

Alfa AF: 0.0878 Hom.: 1894

Bravo AF: 0.0910

Asia WGS AF: 0.0520 AC: 182 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.26
CADD	Benign	21
DANN	Benign	0.79
PhyloP100		3.2

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: rs10490996;

hg19: chr10-80131442;