rs7075349

Variant names:

• chr10-62667889-G-A
• rs7075349
• ENST00000647733.1:c.1294+1687G>A

Variant summary

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

The ENST00000647733.1(ENSG00000285837):​c.1294+1687G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.573 in 151,624 control chromosomes in the GnomAD database, including 26,161 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 0.57 (26161 hom., cov: 29)
• Consequence: ENSG00000285837 ENST00000647733.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0450
• Publications: 9 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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.666 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.1294+1687G>A		intron	N/A	ENSP00000502188.1
	LINC02929	ENST00000344640.7	TSL:1	n.371-2318G>A		intron	N/A
	LINC02929	ENST00000373784.6	TSL:1	n.444+1687G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.573 AC: 86860 AN: 151504 Hom.: 26164 Cov.: 29

Gnomad AFR AF: 0.399

Gnomad AMI AF: 0.831

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.707

Gnomad EAS AF: 0.682

Gnomad SAS AF: 0.520

Gnomad FIN AF: 0.666

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.671

Gnomad OTH AF: 0.595

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

GnomAD4 genome AF: 0.573 AC: 86886 AN: 151624 Hom.: 26161 Cov.: 29 AF XY: 0.570 AC XY: 42255 AN XY: 74088

African (AFR) AF: 0.399 AC: 16465 AN: 41242

American (AMR) AF: 0.471 AC: 7181 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.707 AC: 2453 AN: 3470

East Asian (EAS) AF: 0.682 AC: 3497 AN: 5128

South Asian (SAS) AF: 0.519 AC: 2493 AN: 4800

European-Finnish (FIN) AF: 0.666 AC: 7019 AN: 10532

Middle Eastern (MID) AF: 0.670 AC: 197 AN: 294

European-Non Finnish (NFE) AF: 0.671 AC: 45574 AN: 67890

Other (OTH) AF: 0.595 AC: 1251 AN: 2102

Alfa AF: 0.635 Hom.: 133921

Bravo AF: 0.551

Asia WGS AF: 0.563 AC: 1960 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.2
DANN	Benign	0.71
PhyloP100		0.045
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: rs7075349; hg19: chr10-64427649;