rs7682418

chr4-104507260-G-Achr4-104507260-G-Cchr4-104507260-G-T

Variant summary

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

The NR_125926.1(CXXC4-AS1):n.96+16200G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.272 in 150,866 control chromosomes in the GnomAD database, including 6,083 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 0.27 (6083 hom., cov: 31)
• Consequence: CXXC4-AS1 NR_125926.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.464

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.324 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CXXC4-AS1	NR_125926.1	n.96+16200G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CXXC4-AS1	ENST00000500179.1	n.96+16200G>A		intron_variant, non_coding_transcript_variant		2
CXXC4-AS1	ENST00000664466.1	n.212+16200G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.272 AC: 41009 AN: 150750 Hom.: 6087 Cov.: 31

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.403

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.235

Gnomad EAS AF: 0.0372

Gnomad SAS AF: 0.295

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.327

Gnomad OTH AF: 0.249

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

GnomAD4 genome AF: 0.272 AC: 41003 AN: 150866 Hom.: 6083 Cov.: 31 AF XY: 0.271 AC XY: 20000 AN XY: 73676

Gnomad4 AFR AF: 0.208

Gnomad4 AMR AF: 0.184

Gnomad4 ASJ AF: 0.235

Gnomad4 EAS AF: 0.0367

Gnomad4 SAS AF: 0.296

Gnomad4 FIN AF: 0.400

Gnomad4 NFE AF: 0.327

Gnomad4 OTH AF: 0.246

Alfa AF: 0.301 Hom.: 14431

Bravo AF: 0.248

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	1.6
Dann	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7682418; hg19: chr4-105428417;