rs17034592

Positions:

• chr4-104533803-T-C

Variant summary

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

The ENST00000500179.1(CXXC4-AS1):​n.96+42743T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.216 in 151,978 control chromosomes in the GnomAD database, including 3,789 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 0.22 (3789 hom., cov: 32)
• Consequence: CXXC4-AS1 ENST00000500179.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0450

Genes affected

CXXC4-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.229 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CXXC4-AS1	NR_125926.1	n.96+42743T>C		intron_variant
LOC124900745	XR_007058210.1	n.504-10484A>G		intron_variant
LOC124900745	XR_007058211.1	n.2114-10484A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CXXC4-AS1	ENST00000500179.1	n.96+42743T>C		intron_variant		2
CXXC4-AS1	ENST00000664466.1	n.212+42743T>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.216 AC: 32808 AN: 151860 Hom.: 3791 Cov.: 32

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.234

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.0331

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.307

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.187

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

GnomAD4 genome AF: 0.216 AC: 32809 AN: 151978 Hom.: 3789 Cov.: 32 AF XY: 0.217 AC XY: 16091 AN XY: 74238

Gnomad4 AFR AF: 0.224

Gnomad4 AMR AF: 0.137

Gnomad4 ASJ AF: 0.173

Gnomad4 EAS AF: 0.0326

Gnomad4 SAS AF: 0.212

Gnomad4 FIN AF: 0.307

Gnomad4 NFE AF: 0.232

Gnomad4 OTH AF: 0.184

Alfa AF: 0.217 Hom.: 7417

Bravo AF: 0.200

Asia WGS AF: 0.127 AC: 442 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.1
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17034592; hg19: chr4-105454960;