rs10995195

Variant names:

• chr10-62528630-T-C
• rs10995195
• ENST00000647733.1:c.981+68833T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000647733.1(ENSG00000285837):​c.981+68833T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.18 in 125,678 control chromosomes in the GnomAD database, including 1,797 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 0.18 (1797 hom., cov: 30)
• Consequence: ENSG00000285837 ENST00000647733.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.27

Genes affected

ENSG00000285837 (HGNC:):

LINC02929 (HGNC:55812): (long intergenic non-protein coding RNA 2929)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.191 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
ENSG00000285837	ENST00000647733.1	c.981+68833T>C		intron_variant	Intron 4 of 7			ENSP00000502188.1
LINC02929	ENST00000395251.5	n.150+8033T>C		intron_variant	Intron 1 of 6	1

Frequencies

GnomAD3 genomes AF: 0.180 AC: 22650 AN: 125564 Hom.: 1795 Cov.: 30

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.159

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.0275

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.253

Gnomad MID AF: 0.157

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.182

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

GnomAD4 genome AF: 0.180 AC: 22658 AN: 125678 Hom.: 1797 Cov.: 30 AF XY: 0.182 AC XY: 11075 AN XY: 60986

Gnomad4 AFR AF: 0.171

Gnomad4 AMR AF: 0.159

Gnomad4 ASJ AF: 0.188

Gnomad4 EAS AF: 0.0276

Gnomad4 SAS AF: 0.131

Gnomad4 FIN AF: 0.253

Gnomad4 NFE AF: 0.194

Gnomad4 OTH AF: 0.180

Alfa AF: 0.165 Hom.: 306

Bravo AF: 0.144

Asia WGS AF: 0.0620 AC: 215 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	14
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10995195; hg19: chr10-64288389;