rs10516510

chr4-104516205-G-A

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+25145G>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 0.254 in 151,906 control chromosomes in the GnomAD database, including 5,043 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 (5043 hom., cov: 33)
• Consequence: CXXC4-AS1 NR_125926.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.210

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=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.286 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CXXC4-AS1	NR_125926.1	n.96+25145G>A		intron_variant, non_coding_transcript_variant
LOC124900745	XR_007058211.1	n.3174-128C>T		intron_variant, non_coding_transcript_variant
LOC124900745	XR_007058210.1	n.1564-128C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CXXC4-AS1	ENST00000500179.1	n.96+25145G>A		intron_variant, non_coding_transcript_variant		2
CXXC4-AS1	ENST00000664466.1	n.212+25145G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.254 AC: 38595 AN: 151788 Hom.: 5044 Cov.: 33

Gnomad AFR AF: 0.212

Gnomad AMI AF: 0.353

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.264

Gnomad SAS AF: 0.297

Gnomad FIN AF: 0.355

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.269

Gnomad OTH AF: 0.228

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

GnomAD4 genome AF: 0.254 AC: 38598 AN: 151906 Hom.: 5043 Cov.: 33 AF XY: 0.259 AC XY: 19192 AN XY: 74220

Gnomad4 AFR AF: 0.212

Gnomad4 AMR AF: 0.227

Gnomad4 ASJ AF: 0.202

Gnomad4 EAS AF: 0.263

Gnomad4 SAS AF: 0.299

Gnomad4 FIN AF: 0.355

Gnomad4 NFE AF: 0.269

Gnomad4 OTH AF: 0.225

Alfa AF: 0.257 Hom.: 9971

Bravo AF: 0.242

Asia WGS AF: 0.269 AC: 935 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	2.0
Dann	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10516510; hg19: chr4-105437362;