rs1012178

Variant names:

• chr8-56516957-C-T
• rs1012178
• ENST00000518662.5:n.827+20602C>T

Variant summary

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

The ENST00000518662.5(PENK-AS1):​n.827+20602C>T variant causes a intron 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 ENST00000518662.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.788
• Publications: 3 publications found

Genes affected

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

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000518662.5. 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
	PENK-AS1	NR_125813.1		n.827+20602C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PENK-AS1	ENST00000518662.5	TSL:2	n.827+20602C>T		intron	N/A
	LINC00968	ENST00000519144.5	TSL:4	n.476+3164G>A		intron	N/A
	PENK-AS1	ENST00000522511.1	TSL:4	n.287-7667C>T		intron	N/A

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

African (AFR) AF: 0.0991 AC: 4112 AN: 41508

American (AMR) AF: 0.201 AC: 3066 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.169 AC: 586 AN: 3468

East Asian (EAS) AF: 0.00908 AC: 47 AN: 5178

South Asian (SAS) AF: 0.179 AC: 864 AN: 4828

European-Finnish (FIN) AF: 0.162 AC: 1711 AN: 10582

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.209 AC: 14170 AN: 67960

Other (OTH) AF: 0.172 AC: 363 AN: 2114

Alfa AF: 0.194 Hom.: 5777

Bravo AF: 0.164

Asia WGS AF: 0.125 AC: 437 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.4
DANN	Benign	0.73
PhyloP100		-0.79

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1012178;

hg19: chr8-57429516;