rs2246873

Positions:

• chr8-56521382-G-A
• chr8-56521382-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_038236.1(LINC00968):​n.372-815C>T variant causes a intron, non coding transcript 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 NR_038236.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.93

Genes affected

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

PENK-AS1 (HGNC:55519): (PENK antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC00968	NR_038236.1	n.372-815C>T		intron_variant, non_coding_transcript_variant
PENK-AS1	NR_125813.1	n.827+25027G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00968	ENST00000524338.3	n.372-815C>T		intron_variant, non_coding_transcript_variant		2
PENK-AS1	ENST00000662661.1	n.398-5599G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.384

Gnomad4 AMR AF: 0.494

Gnomad4 ASJ AF: 0.516

Gnomad4 EAS AF: 0.398

Gnomad4 SAS AF: 0.525

Gnomad4 FIN AF: 0.634

Gnomad4 NFE AF: 0.546

Gnomad4 OTH AF: 0.490

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2246873; hg19: chr8-57433941;