rs972583

Positions:

• chr4-104521145-T-C

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+30085T>C 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 0.254 in 151,726 control chromosomes in the GnomAD database, including 5,026 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 0.25 (5026 hom., cov: 32)
• Consequence: CXXC4-AS1 NR_125926.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.855

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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.293 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CXXC4-AS1	NR_125926.1	n.96+30085T>C		intron_variant, non_coding_transcript_variant
LOC124900745	XR_007058211.1	n.2237-789A>G		intron_variant, non_coding_transcript_variant
LOC124900745	XR_007058210.1	n.627-789A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CXXC4-AS1	ENST00000500179.1	n.96+30085T>C		intron_variant, non_coding_transcript_variant		2
CXXC4-AS1	ENST00000664466.1	n.212+30085T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.254 AC: 38502 AN: 151608 Hom.: 5028 Cov.: 32

Gnomad AFR AF: 0.208

Gnomad AMI AF: 0.353

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.210

Gnomad EAS AF: 0.291

Gnomad SAS AF: 0.305

Gnomad FIN AF: 0.344

Gnomad MID AF: 0.188

Gnomad NFE AF: 0.269

Gnomad OTH AF: 0.234

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

GnomAD4 genome AF: 0.254 AC: 38505 AN: 151726 Hom.: 5026 Cov.: 32 AF XY: 0.258 AC XY: 19143 AN XY: 74174

Gnomad4 AFR AF: 0.207

Gnomad4 AMR AF: 0.228

Gnomad4 ASJ AF: 0.210

Gnomad4 EAS AF: 0.290

Gnomad4 SAS AF: 0.306

Gnomad4 FIN AF: 0.344

Gnomad4 NFE AF: 0.269

Gnomad4 OTH AF: 0.231

Alfa AF: 0.266 Hom.: 2529

Bravo AF: 0.242

Asia WGS AF: 0.282 AC: 980 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.20
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs972583; hg19: chr4-105442302;