4-103574893-A-G

Variant names:

• chr4-103574893-A-G
• rs2757673

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

Genes affected

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

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000502936.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TACR3-AS1	NR_186501.1		n.190-16314A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TACR3-AS1	ENST00000502936.1	TSL:2	n.190-16314A>G		intron	N/A
	TACR3-AS1	ENST00000512401.5	TSL:2	n.291+5491A>G		intron	N/A

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

African (AFR) AF: 0.360 AC: 14918 AN: 41474

American (AMR) AF: 0.710 AC: 10848 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.753 AC: 2616 AN: 3472

East Asian (EAS) AF: 0.473 AC: 2438 AN: 5150

South Asian (SAS) AF: 0.591 AC: 2851 AN: 4824

European-Finnish (FIN) AF: 0.809 AC: 8552 AN: 10574

Middle Eastern (MID) AF: 0.704 AC: 207 AN: 294

European-Non Finnish (NFE) AF: 0.749 AC: 50909 AN: 67982

Other (OTH) AF: 0.671 AC: 1415 AN: 2110

Alfa AF: 0.669 Hom.: 6081

Bravo AF: 0.614

Asia WGS AF: 0.544 AC: 1891 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	8.5
DANN	Benign	0.43
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs2757673; hg19: chr4-104496050;