rs12195826

Variant names:

• chr6-2565518-A-G
• rs12195826
• ENST00000840975.1:n.62-1289T>C

Variant summary

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

The ENST00000840975.1(LINC01600):​n.62-1289T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.63 in 152,072 control chromosomes in the GnomAD database, including 30,330 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 0.63 (30330 hom., cov: 31)
• Consequence: LINC01600 ENST00000840975.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.971
• Publications: 9 publications found

Genes affected

LINC01600 (HGNC:21600): (long intergenic non-protein coding RNA 1600)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.665 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000840975.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01600	ENST00000840975.1		n.62-1289T>C		intron	N/A
	LINC01600	ENST00000840976.1		n.359-1289T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.630 AC: 95732 AN: 151954 Hom.: 30315 Cov.: 31

Gnomad AFR AF: 0.572

Gnomad AMI AF: 0.664

Gnomad AMR AF: 0.618

Gnomad ASJ AF: 0.617

Gnomad EAS AF: 0.545

Gnomad SAS AF: 0.589

Gnomad FIN AF: 0.683

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.670

Gnomad OTH AF: 0.608

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

GnomAD4 genome AF: 0.630 AC: 95789 AN: 152072 Hom.: 30330 Cov.: 31 AF XY: 0.627 AC XY: 46591 AN XY: 74318

African (AFR) AF: 0.572 AC: 23727 AN: 41486

American (AMR) AF: 0.618 AC: 9440 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.617 AC: 2140 AN: 3468

East Asian (EAS) AF: 0.544 AC: 2808 AN: 5166

South Asian (SAS) AF: 0.590 AC: 2847 AN: 4828

European-Finnish (FIN) AF: 0.683 AC: 7213 AN: 10558

Middle Eastern (MID) AF: 0.585 AC: 172 AN: 294

European-Non Finnish (NFE) AF: 0.670 AC: 45562 AN: 67974

Other (OTH) AF: 0.605 AC: 1277 AN: 2110

Alfa AF: 0.641 Hom.: 52959

Bravo AF: 0.620

Asia WGS AF: 0.550 AC: 1912 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.96
DANN	Benign	0.49
PhyloP100		-0.97

Splicing

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

Other links and lift over

dbSNP: rs12195826; hg19: chr6-2565752;