rs2082529

Variant names:

• chr12-76033699-T-C
• rs2082529
• ENST00000547721.2:n.1427T>C

Variant summary

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

The ENST00000547721.2(PHLDA1-DT):​n.1427T>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 0.175 in 152,156 control chromosomes in the GnomAD database, including 2,469 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 (2469 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: PHLDA1-DT ENST00000547721.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.414
• Publications: 7 publications found

Genes affected

PHLDA1-DT (HGNC:55470): (PHLDA1 divergent transcript)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.293 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PHLDA1-DT	NR_185978.1	n.1426T>C		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PHLDA1-DT	ENST00000547721.2	n.1427T>C		non_coding_transcript_exon_variant	Exon 2 of 2	2

Frequencies

GnomAD3 genomes AF: 0.175 AC: 26579 AN: 152036 Hom.: 2469 Cov.: 32

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.211

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.246

Gnomad EAS AF: 0.0354

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.193

Gnomad OTH AF: 0.208

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.175 AC: 26591 AN: 152156 Hom.: 2469 Cov.: 32 AF XY: 0.175 AC XY: 13024 AN XY: 74388

African (AFR) AF: 0.140 AC: 5793 AN: 41520

American (AMR) AF: 0.182 AC: 2779 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.246 AC: 852 AN: 3468

East Asian (EAS) AF: 0.0357 AC: 185 AN: 5184

South Asian (SAS) AF: 0.306 AC: 1476 AN: 4816

European-Finnish (FIN) AF: 0.157 AC: 1661 AN: 10580

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.193 AC: 13125 AN: 67986

Other (OTH) AF: 0.207 AC: 437 AN: 2110

Alfa AF: 0.197 Hom.: 4457

Bravo AF: 0.173

Asia WGS AF: 0.171 AC: 595 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.3
DANN	Benign	0.62
PhyloP100		0.41
Mutation Taster		=299/1	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs2082529; hg19: chr12-76427479;