chr2-219400734-C-T

Variant names:

• chr2-219400734-C-T
• rs6436149
• ENST00000420563.1:n.554-1855C>T

Variant summary

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

The ENST00000420563.1(DNPEP-AS1):​n.554-1855C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.866 in 152,226 control chromosomes in the GnomAD database, including 59,529 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 0.87 (59529 hom., cov: 33)
• Consequence: DNPEP-AS1 ENST00000420563.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.21
• Publications: 2 publications found

Genes affected

DNPEP-AS1 (HGNC:55789): (DNPEP antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.981 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DNPEP-AS1	NR_183822.1	n.390-1855C>T		intron_variant	Intron 2 of 2
DNPEP-AS1	NR_183823.1	n.471+330C>T		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DNPEP-AS1	ENST00000420563.1	n.554-1855C>T		intron_variant	Intron 1 of 1	2
DNPEP-AS1	ENST00000729797.1	n.399-1855C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.867 AC: 131813 AN: 152108 Hom.: 59517 Cov.: 33

Gnomad AFR AF: 0.577

Gnomad AMI AF: 0.999

Gnomad AMR AF: 0.944

Gnomad ASJ AF: 0.966

Gnomad EAS AF: 0.905

Gnomad SAS AF: 0.980

Gnomad FIN AF: 0.989

Gnomad MID AF: 0.946

Gnomad NFE AF: 0.987

Gnomad OTH AF: 0.894

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.866 AC: 131854 AN: 152226 Hom.: 59529 Cov.: 33 AF XY: 0.870 AC XY: 64723 AN XY: 74424

African (AFR) AF: 0.576 AC: 23901 AN: 41472

American (AMR) AF: 0.944 AC: 14446 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.966 AC: 3354 AN: 3472

East Asian (EAS) AF: 0.905 AC: 4682 AN: 5174

South Asian (SAS) AF: 0.980 AC: 4731 AN: 4828

European-Finnish (FIN) AF: 0.989 AC: 10507 AN: 10622

Middle Eastern (MID) AF: 0.942 AC: 277 AN: 294

European-Non Finnish (NFE) AF: 0.987 AC: 67153 AN: 68036

Other (OTH) AF: 0.895 AC: 1892 AN: 2114

Alfa AF: 0.919 Hom.: 8172

Bravo AF: 0.849

Asia WGS AF: 0.914 AC: 3179 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.025
DANN	Benign	0.70
PhyloP100		-3.2

Splicing

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

Other links and lift over

dbSNP: rs6436149; hg19: chr2-220265456;