rs2095252

Positions:

• chr6-131962448-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000435287.2(LINC01013):​n.309+11194C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.315 in 152,094 control chromosomes in the GnomAD database, including 9,274 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 0.31 (9274 hom., cov: 32)
• Consequence: LINC01013 ENST00000435287.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.987

Genes affected

LINC01013 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.434 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCN2-AS1	NR_187593.1	n.371+51493C>T		intron_variant
CCN2-AS1	NR_187594.1	n.489-47409C>T		intron_variant
CCN2-AS1	NR_187595.1	n.327+38378C>T		intron_variant
CCN2-AS1	NR_187596.1	n.488+58214C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01013	ENST00000435287.2	n.309+11194C>T		intron_variant		2
LINC01013	ENST00000706294.1	n.183-47409C>T		intron_variant
LINC01013	ENST00000706326.1	n.239+60297C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.315 AC: 47915 AN: 151976 Hom.: 9275 Cov.: 32

Gnomad AFR AF: 0.0860

Gnomad AMI AF: 0.511

Gnomad AMR AF: 0.299

Gnomad ASJ AF: 0.492

Gnomad EAS AF: 0.211

Gnomad SAS AF: 0.409

Gnomad FIN AF: 0.372

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.438

Gnomad OTH AF: 0.342

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

GnomAD4 genome AF: 0.315 AC: 47907 AN: 152094 Hom.: 9274 Cov.: 32 AF XY: 0.313 AC XY: 23298 AN XY: 74338

Gnomad4 AFR AF: 0.0858

Gnomad4 AMR AF: 0.300

Gnomad4 ASJ AF: 0.492

Gnomad4 EAS AF: 0.210

Gnomad4 SAS AF: 0.408

Gnomad4 FIN AF: 0.372

Gnomad4 NFE AF: 0.438

Gnomad4 OTH AF: 0.337

Alfa AF: 0.411 Hom.: 3822

Bravo AF: 0.297

Asia WGS AF: 0.258 AC: 897 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.9
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2095252; hg19: chr6-132283588;