rs10516510

Variant names:

• chr4-104516205-G-A
• rs10516510
• ENST00000500179.1:n.96+25145G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000500179.1(CXXC4-AS1):​n.96+25145G>A variant causes a intron 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 ENST00000500179.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.210
• Publications: 3 publications found

Genes affected

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

LOC124900745 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
CXXC4-AS1	NR_125926.1	n.96+25145G>A		intron_variant	Intron 1 of 9
LOC124900745	XR_007058210.1	n.1564-128C>T		intron_variant	Intron 7 of 7
LOC124900745	XR_007058211.1	n.3174-128C>T		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CXXC4-AS1	ENST00000500179.1	n.96+25145G>A		intron_variant	Intron 1 of 9	2
CXXC4-AS1	ENST00000664466.1	n.212+25145G>A		intron_variant	Intron 1 of 4
CXXC4-AS1	ENST00000723209.1	n.253+25145G>A		intron_variant	Intron 1 of 6

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

African (AFR) AF: 0.212 AC: 8792 AN: 41488

American (AMR) AF: 0.227 AC: 3471 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.202 AC: 703 AN: 3472

East Asian (EAS) AF: 0.263 AC: 1345 AN: 5110

South Asian (SAS) AF: 0.299 AC: 1439 AN: 4820

European-Finnish (FIN) AF: 0.355 AC: 3753 AN: 10558

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.269 AC: 18243 AN: 67874

Other (OTH) AF: 0.225 AC: 477 AN: 2116

Alfa AF: 0.256 Hom.: 15576

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
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs10516510; hg19: chr4-105437362;