rs1866823

Variant names:

• chr8-56524018-G-A
• rs1866823
• ENST00000499425.2:n.220-3451C>T

Your query was ambiguous. Multiple possible variants found:

• chr8-56524018-G-A
• chr8-56524018-G-C

Variant summary

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

The ENST00000499425.2(LINC00968):​n.220-3451C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.47 in 152,008 control chromosomes in the GnomAD database, including 17,881 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 0.47 (17881 hom., cov: 32)
• Consequence: LINC00968 ENST00000499425.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.177
• Publications: 5 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.541 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00968	NR_038236.1	n.372-3451C>T		intron_variant	Intron 1 of 2
PENK-AS1	NR_125813.1	n.828-24275G>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00968	ENST00000499425.2	n.220-3451C>T		intron_variant	Intron 1 of 2	2
PENK-AS1	ENST00000518662.5	n.828-24275G>A		intron_variant	Intron 2 of 3	2
LINC00968	ENST00000518943.1	n.342-3404C>T		intron_variant	Intron 1 of 1	4

Frequencies

GnomAD3 genomes AF: 0.470 AC: 71461 AN: 151888 Hom.: 17879 Cov.: 32

Gnomad AFR AF: 0.299

Gnomad AMI AF: 0.486

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.510

Gnomad EAS AF: 0.398

Gnomad SAS AF: 0.506

Gnomad FIN AF: 0.632

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.546

Gnomad OTH AF: 0.472

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

GnomAD4 genome AF: 0.470 AC: 71493 AN: 152008 Hom.: 17881 Cov.: 32 AF XY: 0.471 AC XY: 35020 AN XY: 74308

African (AFR) AF: 0.299 AC: 12407 AN: 41466

American (AMR) AF: 0.489 AC: 7467 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.510 AC: 1769 AN: 3470

East Asian (EAS) AF: 0.398 AC: 2054 AN: 5164

South Asian (SAS) AF: 0.507 AC: 2436 AN: 4808

European-Finnish (FIN) AF: 0.632 AC: 6674 AN: 10556

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.546 AC: 37097 AN: 67954

Other (OTH) AF: 0.475 AC: 1001 AN: 2108

Alfa AF: 0.516 Hom.: 81830

Bravo AF: 0.451

Asia WGS AF: 0.449 AC: 1567 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.1
DANN	Benign	0.48
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs1866823; hg19: chr8-57436577;