rs7071642

Variant names:

• chr10-62654300-G-A
• rs7071642
• ENST00000647733.1:c.1130-2096G>A

Your query was ambiguous. Multiple possible variants found:

• chr10-62654300-G-A
• chr10-62654300-G-C

Variant summary

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

The ENST00000647733.1(ENSG00000285837):​c.1130-2096G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.812 in 152,134 control chromosomes in the GnomAD database, including 50,928 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 0.81 (50928 hom., cov: 31)
• Consequence: ENSG00000285837 ENST00000647733.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0300
• 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.942 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.1130-2096G>A		intron	N/A	ENSP00000502188.1
	LINC02929	ENST00000344640.7	TSL:1	n.192-543G>A		intron	N/A
	LINC02929	ENST00000373784.6	TSL:1	n.192-543G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.812 AC: 123424 AN: 152016 Hom.: 50869 Cov.: 31

Gnomad AFR AF: 0.950

Gnomad AMI AF: 0.702

Gnomad AMR AF: 0.816

Gnomad ASJ AF: 0.710

Gnomad EAS AF: 0.912

Gnomad SAS AF: 0.869

Gnomad FIN AF: 0.737

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.735

Gnomad OTH AF: 0.786

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

GnomAD4 genome AF: 0.812 AC: 123540 AN: 152134 Hom.: 50928 Cov.: 31 AF XY: 0.813 AC XY: 60463 AN XY: 74354

African (AFR) AF: 0.950 AC: 39461 AN: 41532

American (AMR) AF: 0.817 AC: 12476 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.710 AC: 2462 AN: 3470

East Asian (EAS) AF: 0.913 AC: 4733 AN: 5186

South Asian (SAS) AF: 0.868 AC: 4177 AN: 4812

European-Finnish (FIN) AF: 0.737 AC: 7776 AN: 10556

Middle Eastern (MID) AF: 0.694 AC: 204 AN: 294

European-Non Finnish (NFE) AF: 0.735 AC: 49955 AN: 67978

Other (OTH) AF: 0.783 AC: 1656 AN: 2116

Alfa AF: 0.775 Hom.: 7836

Bravo AF: 0.824

Asia WGS AF: 0.865 AC: 3009 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.2
DANN	Benign	0.33
PhyloP100		-0.030
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: rs7071642; hg19: chr10-64414060;