6-131954297-G-T

Variant names:

• chr6-131954297-G-T
• rs928501
• ENST00000435287.2:n.309+3043G>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000435287.2(LINC01013):​n.309+3043G>T variant causes a intron change. The variant allele was found at a frequency of 0.292 in 152,076 control chromosomes in the GnomAD database, including 6,868 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 0.29 (6868 hom., cov: 32)
• Consequence: LINC01013 ENST00000435287.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.13
• Publications: 6 publications found

Genes affected

LINC01013 (HGNC:48987): (long intergenic non-protein coding RNA 1013)

CCN2-AS1 (HGNC:40164): (CCN2 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.42).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.394 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000435287.2. 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
	CCN2-AS1	NR_187593.1		n.371+43342G>T		intron	N/A
	CCN2-AS1	NR_187594.1		n.488+50063G>T		intron	N/A
	CCN2-AS1	NR_187595.1		n.327+30227G>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01013	ENST00000435287.2	TSL:2	n.309+3043G>T		intron	N/A
	LINC01013	ENST00000440246.2	TSL:3	n.96+4091G>T		intron	N/A
	LINC01013	ENST00000706294.2		n.182+52146G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.292 AC: 44311 AN: 151958 Hom.: 6856 Cov.: 32

Gnomad AFR AF: 0.399

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.243

Gnomad ASJ AF: 0.272

Gnomad EAS AF: 0.120

Gnomad SAS AF: 0.215

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.264

Gnomad OTH AF: 0.302

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

GnomAD4 genome AF: 0.292 AC: 44359 AN: 152076 Hom.: 6868 Cov.: 32 AF XY: 0.287 AC XY: 21359 AN XY: 74356

African (AFR) AF: 0.400 AC: 16560 AN: 41450

American (AMR) AF: 0.243 AC: 3711 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.272 AC: 945 AN: 3468

East Asian (EAS) AF: 0.120 AC: 620 AN: 5180

South Asian (SAS) AF: 0.217 AC: 1048 AN: 4828

European-Finnish (FIN) AF: 0.234 AC: 2479 AN: 10576

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.264 AC: 17973 AN: 67982

Other (OTH) AF: 0.299 AC: 631 AN: 2108

Alfa AF: 0.269 Hom.: 21573

Bravo AF: 0.297

Asia WGS AF: 0.191 AC: 666 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.42
CADD	Benign	19
DANN	Benign	0.84
PhyloP100		4.1

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: rs928501;

hg19: chr6-132275437;