ENST00000499425.1:n.220-815C>T

Variant names:

• chr8-56521382-G-A
• rs2246873
• ENST00000499425.2:n.220-815C>T

Variant summary

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

The ENST00000499425.2(LINC00968):​n.220-815C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.495 in 151,958 control chromosomes in the GnomAD database, including 19,205 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 0.50 (19205 hom., cov: 33)
• Consequence: LINC00968 ENST00000499425.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.93
• Publications: 3 publications found

Genes affected

LINC00968 (HGNC:48727): (long intergenic non-protein coding RNA 968)

PENK-AS1 (HGNC:55519): (PENK 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 (NFE) allele frequency at 95% confidence interval = 0.542 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000499425.2. 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
	LINC00968	NR_038236.1		n.372-815C>T		intron	N/A
	PENK-AS1	NR_125813.1		n.827+25027G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00968	ENST00000499425.2	TSL:2	n.220-815C>T		intron	N/A
	PENK-AS1	ENST00000518662.5	TSL:2	n.827+25027G>A		intron	N/A
	LINC00968	ENST00000518943.1	TSL:4	n.342-768C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.495 AC: 75206 AN: 151840 Hom.: 19201 Cov.: 33

Gnomad AFR AF: 0.384

Gnomad AMI AF: 0.488

Gnomad AMR AF: 0.495

Gnomad ASJ AF: 0.516

Gnomad EAS AF: 0.398

Gnomad SAS AF: 0.524

Gnomad FIN AF: 0.634

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.546

Gnomad OTH AF: 0.488

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

GnomAD4 genome AF: 0.495 AC: 75246 AN: 151958 Hom.: 19205 Cov.: 33 AF XY: 0.495 AC XY: 36758 AN XY: 74262

African (AFR) AF: 0.384 AC: 15900 AN: 41456

American (AMR) AF: 0.494 AC: 7540 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.516 AC: 1790 AN: 3468

East Asian (EAS) AF: 0.398 AC: 2055 AN: 5166

South Asian (SAS) AF: 0.525 AC: 2531 AN: 4822

European-Finnish (FIN) AF: 0.634 AC: 6688 AN: 10548

Middle Eastern (MID) AF: 0.503 AC: 148 AN: 294

European-Non Finnish (NFE) AF: 0.546 AC: 37118 AN: 67938

Other (OTH) AF: 0.490 AC: 1032 AN: 2104

Alfa AF: 0.331 Hom.: 815

Bravo AF: 0.478

Asia WGS AF: 0.455 AC: 1583 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.11
DANN	Benign	0.39
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs2246873; hg19: chr8-57433941;