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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000418220.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DPPA2P2	ENST00000418220.1	TSL:6	n.547G>A		non_coding_transcript_exon	Exon 1 of 1

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4970514;

hg19: chr1-26846195;