8-56516957-C-T

Position:

• chr8-56516957-C-T

Variant summary

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

The NR_125813.1(PENK-AS1):​n.827+20602C>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 0.166 in 152,114 control chromosomes in the GnomAD database, including 2,323 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 0.17 (2323 hom., cov: 32)
• Consequence: PENK-AS1 NR_125813.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.788

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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.206 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PENK-AS1	NR_125813.1	n.827+20602C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00968	ENST00000524338.3	n.818+3164G>A		intron_variant, non_coding_transcript_variant		2
PENK-AS1	ENST00000662661.1	n.398-10024C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.166 AC: 25229 AN: 151996 Hom.: 2321 Cov.: 32

Gnomad AFR AF: 0.0993

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.201

Gnomad ASJ AF: 0.169

Gnomad EAS AF: 0.00906

Gnomad SAS AF: 0.179

Gnomad FIN AF: 0.162

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.171

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

GnomAD4 genome AF: 0.166 AC: 25235 AN: 152114 Hom.: 2323 Cov.: 32 AF XY: 0.163 AC XY: 12122 AN XY: 74376

Gnomad4 AFR AF: 0.0991

Gnomad4 AMR AF: 0.201

Gnomad4 ASJ AF: 0.169

Gnomad4 EAS AF: 0.00908

Gnomad4 SAS AF: 0.179

Gnomad4 FIN AF: 0.162

Gnomad4 NFE AF: 0.209

Gnomad4 OTH AF: 0.172

Alfa AF: 0.200 Hom.: 4377

Bravo AF: 0.164

Asia WGS AF: 0.125 AC: 437 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.4
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1012178; hg19: chr8-57429516;