1-26519704-C-T

Variant names:

• chr1-26519704-C-T
• rs4970514
• ENST00000418220.1:n.547G>A

Variant summary

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

The ENST00000418220.1(DPPA2P2):​n.547G>A 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 0.256 in 1,296,402 control chromosomes in the GnomAD database, including 53,167 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 0.31 (8808 hom., cov: 32)
  • Exomes 𝑓: 0.25 (44359 hom.)
• Consequence: DPPA2P2 ENST00000418220.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0850
• Publications: 4 publications found

Genes affected

DPPA2P2 (HGNC:44627): (developmental pluripotency associated 2 pseudogene 2)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.704 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DPPA2P2		n.26519704C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DPPA2P2	ENST00000418220.1	n.547G>A		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.314 AC: 47686 AN: 151964 Hom.: 8804 Cov.: 32

Gnomad AFR AF: 0.448

Gnomad AMI AF: 0.281

Gnomad AMR AF: 0.330

Gnomad ASJ AF: 0.207

Gnomad EAS AF: 0.723

Gnomad SAS AF: 0.427

Gnomad FIN AF: 0.235

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.299

GnomAD4 exome AF: 0.248 AC: 283762 AN: 1144320 Hom.: 44359 Cov.: 22 AF XY: 0.251 AC XY: 146755 AN XY: 583550

African (AFR) AF: 0.448 AC: 11881 AN: 26528

American (AMR) AF: 0.379 AC: 16725 AN: 44160

Ashkenazi Jewish (ASJ) AF: 0.207 AC: 4992 AN: 24142

East Asian (EAS) AF: 0.755 AC: 28648 AN: 37932

South Asian (SAS) AF: 0.398 AC: 31421 AN: 79002

European-Finnish (FIN) AF: 0.246 AC: 13071 AN: 53234

Middle Eastern (MID) AF: 0.247 AC: 1277 AN: 5162

European-Non Finnish (NFE) AF: 0.197 AC: 162535 AN: 824492

Other (OTH) AF: 0.266 AC: 13212 AN: 49668

GnomAD4 genome AF: 0.314 AC: 47718 AN: 152082 Hom.: 8808 Cov.: 32 AF XY: 0.319 AC XY: 23698 AN XY: 74344

African (AFR) AF: 0.448 AC: 18578 AN: 41464

American (AMR) AF: 0.330 AC: 5032 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.207 AC: 719 AN: 3470

East Asian (EAS) AF: 0.723 AC: 3746 AN: 5180

South Asian (SAS) AF: 0.425 AC: 2048 AN: 4818

European-Finnish (FIN) AF: 0.235 AC: 2486 AN: 10578

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.208 AC: 14137 AN: 67994

Other (OTH) AF: 0.302 AC: 637 AN: 2112

Alfa AF: 0.241 Hom.: 2545

Bravo AF: 0.329

Asia WGS AF: 0.547 AC: 1900 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	7.2
DANN	Benign	0.73
PhyloP100		0.085

Splicing

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

Other links and lift over

dbSNP: rs4970514; hg19: chr1-26846195;