rs500140

chr4-104617315-G-Achr4-104617315-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.97-25696G>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 0.243 in 148,016 control chromosomes in the GnomAD database, including 4,591 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 0.24 (4591 hom., cov: 30)
• Consequence: CXXC4-AS1 NR_125926.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.261

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=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.276 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CXXC4-AS1	NR_125926.1	n.97-25696G>A		intron_variant, non_coding_transcript_variant
LOC124900745	XR_007058211.1	n.2113+36512C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CXXC4-AS1	ENST00000500179.1	n.97-25696G>A		intron_variant, non_coding_transcript_variant		2
CXXC4-AS1	ENST00000664466.1	n.213-20583G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.243 AC: 35984 AN: 147924 Hom.: 4585 Cov.: 30

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.424

Gnomad AMR AF: 0.283

Gnomad ASJ AF: 0.258

Gnomad EAS AF: 0.273

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.270

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.272

Gnomad OTH AF: 0.254

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

GnomAD4 genome AF: 0.243 AC: 35997 AN: 148016 Hom.: 4591 Cov.: 30 AF XY: 0.242 AC XY: 17383 AN XY: 71932

Gnomad4 AFR AF: 0.177

Gnomad4 AMR AF: 0.283

Gnomad4 ASJ AF: 0.258

Gnomad4 EAS AF: 0.272

Gnomad4 SAS AF: 0.122

Gnomad4 FIN AF: 0.270

Gnomad4 NFE AF: 0.272

Gnomad4 OTH AF: 0.261

Alfa AF: 0.133 Hom.: 257

Bravo AF: 0.240

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	2.4
Dann	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs500140; hg19: chr4-105538472;