10-62648607-C-T

Variant names:

• chr10-62648607-C-T
• rs7068361
• ENST00000647733.1:c.1130-7789C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000647733.1(ENSG00000285837):​c.1130-7789C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.557 in 152,064 control chromosomes in the GnomAD database, including 23,714 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 0.56 (23714 hom., cov: 32)
• Consequence: ENSG00000285837 ENST00000647733.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.51
• Publications: 3 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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.639 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.1130-7789C>T		intron	N/A	ENSP00000502188.1
	LINC02929	ENST00000344640.7	TSL:1	n.191+4644C>T		intron	N/A
	LINC02929	ENST00000373784.6	TSL:1	n.191+4644C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.558 AC: 84720 AN: 151946 Hom.: 23700 Cov.: 32

Gnomad AFR AF: 0.548

Gnomad AMI AF: 0.563

Gnomad AMR AF: 0.473

Gnomad ASJ AF: 0.537

Gnomad EAS AF: 0.657

Gnomad SAS AF: 0.620

Gnomad FIN AF: 0.575

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.569

Gnomad OTH AF: 0.548

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

GnomAD4 genome AF: 0.557 AC: 84766 AN: 152064 Hom.: 23714 Cov.: 32 AF XY: 0.557 AC XY: 41428 AN XY: 74320

African (AFR) AF: 0.548 AC: 22725 AN: 41456

American (AMR) AF: 0.473 AC: 7230 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.537 AC: 1862 AN: 3470

East Asian (EAS) AF: 0.658 AC: 3408 AN: 5182

South Asian (SAS) AF: 0.620 AC: 2991 AN: 4828

European-Finnish (FIN) AF: 0.575 AC: 6067 AN: 10554

Middle Eastern (MID) AF: 0.565 AC: 166 AN: 294

European-Non Finnish (NFE) AF: 0.569 AC: 38655 AN: 67970

Other (OTH) AF: 0.545 AC: 1150 AN: 2112

Alfa AF: 0.560 Hom.: 90625

Bravo AF: 0.550

Asia WGS AF: 0.607 AC: 2112 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.33
DANN	Benign	0.37
PhyloP100		-1.5
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: rs7068361; hg19: chr10-64408367;