chr1-87958283-T-C

Variant names:

• chr1-87958283-T-C
• rs2991716
• ENST00000731723.1:n.11T>C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000731723.1(ENSG00000295677):​n.11T>C 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 0.46 in 152,012 control chromosomes in the GnomAD database, including 16,386 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 0.46 (16386 hom., cov: 32)
• Consequence: ENSG00000295677 ENST00000731723.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.14
• Publications: 6 publications found

Genes affected

ENSG00000295677 (HGNC:):

PKN2-AS1 (HGNC:50597): (PKN2 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.22).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.578 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000295677	ENST00000731723.1	n.11T>C		non_coding_transcript_exon_variant	Exon 1 of 5
ENSG00000295677	ENST00000731734.1	n.205T>C		non_coding_transcript_exon_variant	Exon 3 of 4
ENSG00000295677	ENST00000731745.1	n.16T>C		non_coding_transcript_exon_variant	Exon 1 of 3

Frequencies

GnomAD3 genomes AF: 0.460 AC: 69828 AN: 151894 Hom.: 16364 Cov.: 32

Gnomad AFR AF: 0.403

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.468

Gnomad ASJ AF: 0.461

Gnomad EAS AF: 0.393

Gnomad SAS AF: 0.597

Gnomad FIN AF: 0.518

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.480

Gnomad OTH AF: 0.457

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

GnomAD4 genome AF: 0.460 AC: 69879 AN: 152012 Hom.: 16386 Cov.: 32 AF XY: 0.464 AC XY: 34453 AN XY: 74302

African (AFR) AF: 0.403 AC: 16715 AN: 41454

American (AMR) AF: 0.469 AC: 7161 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.461 AC: 1599 AN: 3470

East Asian (EAS) AF: 0.393 AC: 2030 AN: 5166

South Asian (SAS) AF: 0.596 AC: 2873 AN: 4818

European-Finnish (FIN) AF: 0.518 AC: 5470 AN: 10562

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.480 AC: 32652 AN: 67956

Other (OTH) AF: 0.462 AC: 975 AN: 2110

Alfa AF: 0.476 Hom.: 34364

Bravo AF: 0.452

Asia WGS AF: 0.520 AC: 1805 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.22
CADD	Benign	18
DANN	Benign	0.85
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs2991716; hg19: chr1-88423966;