10-62528630-T-C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

Genes affected

ENSG00000285837 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000647733.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285837	ENST00000647733.1		c.981+68833T>C		intron	N/A	ENSP00000502188.1
	LINC02929	ENST00000395251.5	TSL:1	n.150+8033T>C		intron	N/A

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

African (AFR) AF: 0.171 AC: 6683 AN: 39066

American (AMR) AF: 0.159 AC: 1734 AN: 10904

Ashkenazi Jewish (ASJ) AF: 0.188 AC: 531 AN: 2832

East Asian (EAS) AF: 0.0276 AC: 112 AN: 4062

South Asian (SAS) AF: 0.131 AC: 403 AN: 3076

European-Finnish (FIN) AF: 0.253 AC: 2213 AN: 8732

Middle Eastern (MID) AF: 0.143 AC: 30 AN: 210

European-Non Finnish (NFE) AF: 0.194 AC: 10535 AN: 54330

Other (OTH) AF: 0.180 AC: 304 AN: 1690

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	14
DANN	Benign	0.80
PhyloP100		2.3
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs10995195; hg19: chr10-64288389;