rs6907728

Variant names:

• chr6-131907629-A-C
• rs6907728
• ENST00000421310.6:n.601+99A>C

Your query was ambiguous. Multiple possible variants found:

• chr6-131907629-A-C
• chr6-131907629-A-G

Variant summary

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

The ENST00000454596.2(LINC01013):​n.189+5478A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.165 in 151,954 control chromosomes in the GnomAD database, including 2,845 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 (2844 hom., cov: 32)
  • Exomes 𝑓: 0.14 (1 hom.)
• Consequence: LINC01013 ENST00000454596.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.480
• Publications: 5 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.305 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000454596.2. 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.201-3156A>C		intron	N/A
	CCN2-AS1	NR_187594.1		n.488+3395A>C		intron	N/A
	CCN2-AS1	NR_187595.1		n.200+5478A>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01013	ENST00000421310.6	TSL:5	n.601+99A>C		intron	N/A
	LINC01013	ENST00000454596.2	TSL:2	n.189+5478A>C		intron	N/A
	LINC01013	ENST00000706294.2		n.182+5478A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.165 AC: 25032 AN: 151790 Hom.: 2835 Cov.: 32

Gnomad AFR AF: 0.309

Gnomad AMI AF: 0.0703

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.272

Gnomad SAS AF: 0.0855

Gnomad FIN AF: 0.0663

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0958

Gnomad OTH AF: 0.163

GnomAD4 exome AF: 0.143 AC: 6 AN: 42 Hom.: 1 AF XY: 0.147 AC XY: 5 AN XY: 34

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AF: 1.00 AC: 2 AN: 2

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.118 AC: 4 AN: 34

Other (OTH) AF: 0.00 AC: 0 AN: 2

GnomAD4 genome AF: 0.165 AC: 25085 AN: 151912 Hom.: 2844 Cov.: 32 AF XY: 0.162 AC XY: 12070 AN XY: 74278

African (AFR) AF: 0.309 AC: 12780 AN: 41352

American (AMR) AF: 0.152 AC: 2323 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.147 AC: 509 AN: 3470

East Asian (EAS) AF: 0.273 AC: 1405 AN: 5150

South Asian (SAS) AF: 0.0858 AC: 413 AN: 4814

European-Finnish (FIN) AF: 0.0663 AC: 702 AN: 10596

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.0958 AC: 6513 AN: 67956

Other (OTH) AF: 0.163 AC: 344 AN: 2106

Alfa AF: 0.122 Hom.: 5716

Bravo AF: 0.181

Asia WGS AF: 0.190 AC: 660 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.9
DANN	Benign	0.62
PhyloP100		0.48

Splicing

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

Other links and lift over

dbSNP: rs6907728; hg19: chr6-132228769;