rs12744840

chr1-31645500-T-C

Variant summary

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

The NR_184311.1(PEF1-AS1):n.296+654T>C 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 0.0434 in 153,428 control chromosomes in the GnomAD database, including 209 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 0.044 (209 hom., cov: 32)
  • Exomes 𝑓: 0.021 (0 hom.)
• Consequence: PEF1-AS1 NR_184311.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.324

Genes affected

(HGNC:):

PEF1-AS1 (HGNC:40154): (PEF1 and COL16A1 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0656 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PEF1-AS1	NR_184311.1	n.296+654T>C		intron_variant, non_coding_transcript_variant
PEF1-AS1	NR_184312.1	n.296+654T>C		intron_variant, non_coding_transcript_variant
PEF1-AS1	NR_184313.1	n.296+654T>C		intron_variant, non_coding_transcript_variant
PEF1-AS1	NR_184314.1	n.326+118T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000581333.1	n.153+654T>C		intron_variant, non_coding_transcript_variant		4
PEF1-AS1	ENST00000609549.5	n.248+1204T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0436 AC: 6635 AN: 152122 Hom.: 209 Cov.: 32

Gnomad AFR AF: 0.0116

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.0373

Gnomad ASJ AF: 0.0311

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.00580

Gnomad FIN AF: 0.0619

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0672

Gnomad OTH AF: 0.0412

GnomAD4 exome AF: 0.0210 AC: 25 AN: 1188 Hom.: 0 AF XY: 0.0176 AC XY: 13 AN XY: 740

Gnomad4 AMR exome AF: 0.00617

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00725

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0452

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0436 AC: 6631 AN: 152240 Hom.: 209 Cov.: 32 AF XY: 0.0421 AC XY: 3131 AN XY: 74430

Gnomad4 AFR AF: 0.0116

Gnomad4 AMR AF: 0.0372

Gnomad4 ASJ AF: 0.0311

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.00560

Gnomad4 FIN AF: 0.0619

Gnomad4 NFE AF: 0.0672

Gnomad4 OTH AF: 0.0408

Alfa AF: 0.0604 Hom.: 47

Bravo AF: 0.0404

Asia WGS AF: 0.00577 AC: 20 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	14
Dann	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12744840; hg19: chr1-32111101;