rs1530217

Variant names:

• chr8-56495538-C-T
• rs1530217
• ENST00000523664.3:n.1543G>A

Variant summary

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

The ENST00000523664.3(LINC00968):​n.1543G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.823 in 152,168 control chromosomes in the GnomAD database, including 51,981 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 0.82 (51981 hom., cov: 31)
• Consequence: LINC00968 ENST00000523664.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.04
• Publications: 1 publications found

Genes affected

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

LOC101929398 (HGNC:):

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 (AFR) allele frequency at 95% confidence interval = 0.918 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101929398	XR_001745919.1	n.1268G>A		non_coding_transcript_exon_variant	Exon 2 of 2
PENK-AS1	NR_125813.1	n.695-685C>T		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00968	ENST00000523664.3	n.1543G>A		non_coding_transcript_exon_variant	Exon 3 of 3	4
LINC00968	ENST00000524338.3	n.1614G>A		non_coding_transcript_exon_variant	Exon 3 of 3	2
LINC00968	ENST00000692050.2	n.1430G>A		non_coding_transcript_exon_variant	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.823 AC: 125181 AN: 152050 Hom.: 51933 Cov.: 31

Gnomad AFR AF: 0.927

Gnomad AMI AF: 0.803

Gnomad AMR AF: 0.825

Gnomad ASJ AF: 0.798

Gnomad EAS AF: 0.870

Gnomad SAS AF: 0.855

Gnomad FIN AF: 0.800

Gnomad MID AF: 0.813

Gnomad NFE AF: 0.760

Gnomad OTH AF: 0.812

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

GnomAD4 genome AF: 0.823 AC: 125291 AN: 152168 Hom.: 51981 Cov.: 31 AF XY: 0.823 AC XY: 61240 AN XY: 74386

African (AFR) AF: 0.926 AC: 38467 AN: 41530

American (AMR) AF: 0.826 AC: 12620 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.798 AC: 2771 AN: 3472

East Asian (EAS) AF: 0.869 AC: 4497 AN: 5172

South Asian (SAS) AF: 0.857 AC: 4125 AN: 4816

European-Finnish (FIN) AF: 0.800 AC: 8471 AN: 10590

Middle Eastern (MID) AF: 0.816 AC: 240 AN: 294

European-Non Finnish (NFE) AF: 0.760 AC: 51644 AN: 67982

Other (OTH) AF: 0.815 AC: 1725 AN: 2116

Alfa AF: 0.799 Hom.: 6072

Bravo AF: 0.829

Asia WGS AF: 0.883 AC: 3073 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.21
DANN	Benign	0.52
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs1530217; hg19: chr8-57408097;