rs7768619

Variant names:

• chr6-131956193-T-C
• rs7768619
• ENST00000435287.2:n.309+4939T>C

Your query was ambiguous. Multiple possible variants found:

• chr6-131956193-T-C
• chr6-131956193-T-G

Variant summary

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

The ENST00000435287.2(LINC01013):​n.309+4939T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.172 in 152,170 control chromosomes in the GnomAD database, including 2,693 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 0.17 (2693 hom., cov: 32)
• Consequence: LINC01013 ENST00000435287.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.152
• Publications: 4 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.388 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+45238T>C		intron	N/A
	CCN2-AS1	NR_187594.1		n.488+51959T>C		intron	N/A
	CCN2-AS1	NR_187595.1		n.327+32123T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01013	ENST00000435287.2	TSL:2	n.309+4939T>C		intron	N/A
	LINC01013	ENST00000440246.2	TSL:3	n.96+5987T>C		intron	N/A
	LINC01013	ENST00000706294.2		n.183-53664T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.172 AC: 26137 AN: 152052 Hom.: 2686 Cov.: 32

Gnomad AFR AF: 0.0811

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.100

Gnomad EAS AF: 0.403

Gnomad SAS AF: 0.270

Gnomad FIN AF: 0.219

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.192

Gnomad OTH AF: 0.169

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

GnomAD4 genome AF: 0.172 AC: 26164 AN: 152170 Hom.: 2693 Cov.: 32 AF XY: 0.177 AC XY: 13152 AN XY: 74384

African (AFR) AF: 0.0813 AC: 3376 AN: 41536

American (AMR) AF: 0.209 AC: 3196 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.100 AC: 347 AN: 3470

East Asian (EAS) AF: 0.403 AC: 2078 AN: 5160

South Asian (SAS) AF: 0.270 AC: 1299 AN: 4818

European-Finnish (FIN) AF: 0.219 AC: 2322 AN: 10586

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.192 AC: 13024 AN: 67996

Other (OTH) AF: 0.175 AC: 370 AN: 2114

Alfa AF: 0.186 Hom.: 9752

Bravo AF: 0.169

Asia WGS AF: 0.346 AC: 1202 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	7.3
DANN	Benign	0.86
PhyloP100		-0.15

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: rs7768619;

hg19: chr6-132277333;