4-103574893-A-G

Position:

• chr4-103574893-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.628 in 152,066 control chromosomes in the GnomAD database, including 32,449 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 0.63 (32449 hom., cov: 33)
• Consequence: DDX3P3 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.47

Genes affected

DDX3P3 (HGNC:42173): (DEAD-box helicase 3 pseudogene 3)

TACR3-AS1 (HGNC:55593): (TACR3 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.743 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DDX3P3		n.103574893A>G		intragenic_variant
TACR3-AS1	NR_186501.1	n.190-16314A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TACR3-AS1	ENST00000502936.1	n.190-16314A>G		intron_variant		2
TACR3-AS1	ENST00000512401.5	n.291+5491A>G		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.628 AC: 95481 AN: 151948 Hom.: 32440 Cov.: 33

Gnomad AFR AF: 0.360

Gnomad AMI AF: 0.841

Gnomad AMR AF: 0.710

Gnomad ASJ AF: 0.753

Gnomad EAS AF: 0.474

Gnomad SAS AF: 0.591

Gnomad FIN AF: 0.809

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.749

Gnomad OTH AF: 0.670

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

GnomAD4 genome AF: 0.628 AC: 95521 AN: 152066 Hom.: 32449 Cov.: 33 AF XY: 0.631 AC XY: 46902 AN XY: 74324

Gnomad4 AFR AF: 0.360

Gnomad4 AMR AF: 0.710

Gnomad4 ASJ AF: 0.753

Gnomad4 EAS AF: 0.473

Gnomad4 SAS AF: 0.591

Gnomad4 FIN AF: 0.809

Gnomad4 NFE AF: 0.749

Gnomad4 OTH AF: 0.671

Alfa AF: 0.679 Hom.: 6024

Bravo AF: 0.614

Asia WGS AF: 0.544 AC: 1891 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	8.5
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2757673; hg19: chr4-104496050;