rs12744840

Variant names:

• chr1-31645500-T-C
• rs12744840
• ENST00000820366.1:n.1072T>C

Variant summary

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

The ENST00000820366.1(PEF1-AS1):​n.1072T>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 0.0434 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 ENST00000820366.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.324
• Publications: 1 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
PEF1-AS1	NR_184311.1	n.296+654T>C		intron_variant	Intron 2 of 5
PEF1-AS1	NR_184312.1	n.296+654T>C		intron_variant	Intron 2 of 4
PEF1-AS1	NR_184313.1	n.296+654T>C		intron_variant	Intron 2 of 5
PEF1-AS1	NR_184314.1	n.326+118T>C		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PEF1-AS1	ENST00000820366.1	n.1072T>C		non_coding_transcript_exon_variant	Exon 3 of 3
PEF1-AS1	ENST00000581333.2	n.188+654T>C		intron_variant	Intron 1 of 1	4
PEF1-AS1	ENST00000585413.5	n.130+118T>C		intron_variant	Intron 1 of 4	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

African (AFR) AC: 0 AN: 0

American (AMR) AF: 0.00617 AC: 1 AN: 162

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 6

East Asian (EAS) AF: 0.00 AC: 0 AN: 4

South Asian (SAS) AF: 0.00725 AC: 4 AN: 552

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.0452 AC: 20 AN: 442

Other (OTH) AF: 0.00 AC: 0 AN: 18

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

African (AFR) AF: 0.0116 AC: 480 AN: 41544

American (AMR) AF: 0.0372 AC: 569 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0311 AC: 108 AN: 3468

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5186

South Asian (SAS) AF: 0.00560 AC: 27 AN: 4820

European-Finnish (FIN) AF: 0.0619 AC: 656 AN: 10598

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.0672 AC: 4572 AN: 68014

Other (OTH) AF: 0.0408 AC: 86 AN: 2108

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
PhyloP100		0.32
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs12744840; hg19: chr1-32111101;