chr10-62655424-A-G

Variant names:

• chr10-62655424-A-G
• rs7076156
• ENST00000395251.5:n.518A>G

Variant summary

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

The ENST00000395251.5(LINC02929):​n.518A>G variant causes a non coding transcript exon 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: LINC02929 ENST00000395251.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.25
• Publications: 73 publications found

Genes affected

LINC02929 (HGNC:55812): (long intergenic non-protein coding RNA 2929)

ENSG00000285837 (HGNC:):

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902436	XM_047426121.1	c.340A>G	p.Thr114Ala	missense_variant	Exon 3 of 6		XP_047282077.1
LOC124902436	XM_047426118.1	c.340A>G	p.Thr114Ala	missense_variant	Exon 3 of 6		XP_047282074.1
LOC124902436	XM_047426119.1	c.340A>G	p.Thr114Ala	missense_variant	Exon 3 of 5		XP_047282075.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285837	ENST00000647733.1	c.1130-972A>G		intron_variant	Intron 5 of 7			ENSP00000502188.1

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

TwinsUK AF: 0.746 AC: 2768

ALSPAC AF: 0.740 AC: 2852

ESP6500AA AF: 0.946 AC: 4167

ESP6500EA AF: 0.734 AC: 6311

ExAC AF: 0.794 AC: 96363

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 v4.3

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
Vest4		0.0050
ClinPred		0.0013	T
GERP RS		-6.8
Mutation Taster		=99/1	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs7076156; hg19: chr10-64415184; COSMIC: COSV107432914;