10-62655424-A-G

Variant names:

• chr10-62655424-A-G
• rs7076156
• ENST00000647733.1:c.1130-972A>G

Variant summary

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

The ENST00000647733.1(ENSG00000285837):​c.1130-972A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.765 in 1,613,968 control chromosomes in the GnomAD database, including 475,776 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 (50907 hom., cov: 31)
  • Exomes 𝑓: 0.76 (424869 hom.)
• Consequence: ENSG00000285837 ENST00000647733.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.25
• Publications: 74 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 (MetaRNN=6.7336487E-7).
• 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285837	ENST00000647733.1		c.1130-972A>G		intron	N/A	ENSP00000502188.1
	LINC02929	ENST00000395251.5	TSL:1	n.518A>G		non_coding_transcript_exon	Exon 4 of 7
	LINC02929	ENST00000461412.1	TSL:1	n.239A>G		non_coding_transcript_exon	Exon 3 of 5

Frequencies

GnomAD3 genomes AF: 0.812 AC: 123385 AN: 151986 Hom.: 50848 Cov.: 31

Gnomad AFR AF: 0.950

Gnomad AMI AF: 0.703

Gnomad AMR AF: 0.816

Gnomad ASJ AF: 0.707

Gnomad EAS AF: 0.912

Gnomad SAS AF: 0.871

Gnomad FIN AF: 0.737

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.735

Gnomad OTH AF: 0.785

GnomAD2 exomes AF: 0.797 AC: 200272 AN: 251422 AF XY: 0.791

Gnomad AFR exome AF: 0.954

Gnomad AMR exome AF: 0.871

Gnomad ASJ exome AF: 0.720

Gnomad EAS exome AF: 0.909

Gnomad FIN exome AF: 0.751

Gnomad NFE exome AF: 0.732

Gnomad OTH exome AF: 0.763

GnomAD4 exome AF: 0.760 AC: 1110768 AN: 1461864 Hom.: 424869 Cov.: 68 AF XY: 0.761 AC XY: 553436 AN XY: 727232

African (AFR) AF: 0.954 AC: 31952 AN: 33480

American (AMR) AF: 0.864 AC: 38622 AN: 44724

Ashkenazi Jewish (ASJ) AF: 0.716 AC: 18722 AN: 26136

East Asian (EAS) AF: 0.924 AC: 36672 AN: 39698

South Asian (SAS) AF: 0.864 AC: 74551 AN: 86258

European-Finnish (FIN) AF: 0.749 AC: 40037 AN: 53420

Middle Eastern (MID) AF: 0.704 AC: 4060 AN: 5768

European-Non Finnish (NFE) AF: 0.737 AC: 819623 AN: 1111986

Other (OTH) AF: 0.770 AC: 46529 AN: 60394

GnomAD4 genome AF: 0.812 AC: 123501 AN: 152104 Hom.: 50907 Cov.: 31 AF XY: 0.813 AC XY: 60465 AN XY: 74362

African (AFR) AF: 0.950 AC: 39421 AN: 41502

American (AMR) AF: 0.817 AC: 12482 AN: 15284

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

East Asian (EAS) AF: 0.913 AC: 4728 AN: 5178

South Asian (SAS) AF: 0.870 AC: 4198 AN: 4828

European-Finnish (FIN) AF: 0.737 AC: 7793 AN: 10578

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

European-Non Finnish (NFE) AF: 0.735 AC: 49932 AN: 67950

Other (OTH) AF: 0.782 AC: 1650 AN: 2110

Alfa AF: 0.759 Hom.: 220115

Bravo AF: 0.824

Asia WGS AF: 0.867 AC: 3016 AN: 3478

EpiCase AF: 0.733

EpiControl AF: 0.729

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.067
BayesDel_addAF	Benign	-0.79	T
BayesDel_noAF	Benign	-0.77
CADD	Benign	0.034
DANN	Benign	0.48
Eigen	Benign	-1.9
Eigen_PC	Benign	-2.0
FATHMM_MKL	Benign	0.0024	N
LIST_S2	Benign	0.11	T
MetaRNN	Benign	6.7e-7	T
MetaSVM	Benign	-0.99	T
PhyloP100		-2.2
Sift4G	Benign	0.91	T
Mutation Taster		=99/1	polymorphism (auto)

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7076156;

hg19: chr10-64415184;

COSMIC: COSV107432914;