rs6852312

Variant names:

• chr4-104593013-C-A
• rs6852312
• ENST00000500179.1:n.97-49998C>A

Variant summary

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

The ENST00000500179.1(CXXC4-AS1):​n.97-49998C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.156 in 152,040 control chromosomes in the GnomAD database, including 3,059 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 0.16 (3059 hom., cov: 32)
• Consequence: CXXC4-AS1 ENST00000500179.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.234

Genes affected

CXXC4-AS1 (HGNC:41054): (CXXC4 antisense RNA 1)

LOC124900745 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.35 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CXXC4-AS1	NR_125926.1	n.97-49998C>A		intron_variant	Intron 1 of 9
LOC124900745	XR_007058211.1	n.2113+60814G>T		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CXXC4-AS1	ENST00000500179.1	n.97-49998C>A		intron_variant	Intron 1 of 9	2
CXXC4-AS1	ENST00000664466.1	n.213-44885C>A		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.155 AC: 23616 AN: 151922 Hom.: 3034 Cov.: 32

Gnomad AFR AF: 0.354

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.123

Gnomad ASJ AF: 0.0312

Gnomad EAS AF: 0.0275

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.0600

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0795

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.156 AC: 23690 AN: 152040 Hom.: 3059 Cov.: 32 AF XY: 0.153 AC XY: 11342 AN XY: 74336

Gnomad4 AFR AF: 0.355

Gnomad4 AMR AF: 0.123

Gnomad4 ASJ AF: 0.0312

Gnomad4 EAS AF: 0.0277

Gnomad4 SAS AF: 0.113

Gnomad4 FIN AF: 0.0600

Gnomad4 NFE AF: 0.0795

Gnomad4 OTH AF: 0.115

Alfa AF: 0.108 Hom.: 516

Bravo AF: 0.167

Asia WGS AF: 0.100 AC: 348 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	3.8
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6852312; hg19: chr4-105514170;