10-62528371-G-C

Variant names:

• chr10-62528371-G-C
• rs10995194
• ENST00000647733.1:c.981+68574G>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+68574G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.142 in 152,184 control chromosomes in the GnomAD database, including 1,599 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 0.14 (1599 hom., cov: 32)
• Consequence: ENSG00000285837 ENST00000647733.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.732
• Publications: 10 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=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.153 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285837	ENST00000647733.1		c.981+68574G>C		intron	N/A	ENSP00000502188.1
	LINC02929	ENST00000395251.5	TSL:1	n.150+7774G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.142 AC: 21611 AN: 152066 Hom.: 1597 Cov.: 32

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.0214

Gnomad SAS AF: 0.0855

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.142 AC: 21623 AN: 152184 Hom.: 1599 Cov.: 32 AF XY: 0.143 AC XY: 10655 AN XY: 74412

African (AFR) AF: 0.132 AC: 5500 AN: 41514

American (AMR) AF: 0.111 AC: 1691 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.154 AC: 535 AN: 3470

East Asian (EAS) AF: 0.0214 AC: 111 AN: 5180

South Asian (SAS) AF: 0.0858 AC: 414 AN: 4826

European-Finnish (FIN) AF: 0.222 AC: 2351 AN: 10590

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.156 AC: 10591 AN: 67994

Other (OTH) AF: 0.137 AC: 289 AN: 2108

Alfa AF: 0.161 Hom.: 240

Bravo AF: 0.134

Asia WGS AF: 0.0590 AC: 204 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	1.9
DANN	Benign	0.80
PhyloP100		0.73
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: rs10995194; hg19: chr10-64288130;