chr7-49258329-G-A

Variant names:

• chr7-49258329-G-A
• rs10485949
• ENST00000604753.1:n.*164C>T

Variant summary

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

The ENST00000604753.1(DDX43P2):​n.*164C>T variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0929 in 151,958 control chromosomes in the GnomAD database, including 741 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 0.093 (741 hom., cov: 33)
• Consequence: DDX43P2 ENST00000604753.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.31
• Publications: 0 publications found

Genes affected

DDX43P2 (HGNC:50781): (DEAD-box helicase 43 pseudogene 2)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.158 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DDX43P2	ENST00000604753.1	n.*164C>T		downstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.0928 AC: 14098 AN: 151842 Hom.: 739 Cov.: 33

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.0471

Gnomad ASJ AF: 0.0282

Gnomad EAS AF: 0.167

Gnomad SAS AF: 0.0980

Gnomad FIN AF: 0.145

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0757

Gnomad OTH AF: 0.0798

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

GnomAD4 genome AF: 0.0929 AC: 14120 AN: 151958 Hom.: 741 Cov.: 33 AF XY: 0.0954 AC XY: 7088 AN XY: 74274

African (AFR) AF: 0.123 AC: 5100 AN: 41424

American (AMR) AF: 0.0469 AC: 715 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.0282 AC: 98 AN: 3472

East Asian (EAS) AF: 0.167 AC: 865 AN: 5176

South Asian (SAS) AF: 0.0989 AC: 476 AN: 4814

European-Finnish (FIN) AF: 0.145 AC: 1531 AN: 10524

Middle Eastern (MID) AF: 0.0274 AC: 8 AN: 292

European-Non Finnish (NFE) AF: 0.0757 AC: 5145 AN: 67976

Other (OTH) AF: 0.0813 AC: 172 AN: 2116

Alfa AF: 0.0470 Hom.: 55

Bravo AF: 0.0866

Asia WGS AF: 0.114 AC: 397 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.050
DANN	Benign	0.49
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs10485949; hg19: chr7-49297925;