rs7076156

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr10-62655424-A-C
• chr10-62655424-A-G
• chr10-62655424-A-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000647733.1(ENSG00000285837):​c.1130-972A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
• Consequence: ENSG00000285837 ENST00000647733.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.25

Genes affected

ENSG00000285837 (HGNC:):

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

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.04224795).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902436	XM_047426121.1	c.340A>C	p.Thr114Pro	missense_variant	Exon 3 of 6		XP_047282077.1
LOC124902436	XM_047426118.1	c.340A>C	p.Thr114Pro	missense_variant	Exon 3 of 6		XP_047282074.1
LOC124902436	XM_047426119.1	c.340A>C	p.Thr114Pro	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>C		intron_variant	Intron 5 of 7			ENSP00000502188.1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 68

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Benign	-0.25	T
BayesDel_noAF	Benign	-0.60
CADD	Benign	0.037
DANN	Benign	0.53
Eigen	Benign	-1.9
Eigen_PC	Benign	-2.0
FATHMM_MKL	Benign	0.014	N
LIST_S2	Benign	0.096	T
M_CAP	Benign	0.0048	T
MetaRNN	Benign	0.042	T
MetaSVM	Benign	-0.99	T
Sift4G	Benign	0.10	T
Vest4		0.10
MutPred		0.22		Loss of sheet (P = 0.0228);
MVP		0.048
ClinPred		0.076	T
GERP RS		-6.8

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7076156; hg19: chr10-64415184;