rs972583

Variant names:

• chr4-104521145-T-C
• rs972583
• ENST00000500179.1:n.96+30085T>C

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+30085T>C 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 151,726 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 ENST00000500179.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.855
• Publications: 0 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=-0.91).
• 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 rank	MANE	Protein	UniProt
CXXC4-AS1	NR_125926.1	n.96+30085T>C		intron_variant	Intron 1 of 9
LOC124900745	XR_007058210.1	n.627-789A>G		intron_variant	Intron 5 of 7
LOC124900745	XR_007058211.1	n.2237-789A>G		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CXXC4-AS1	ENST00000500179.1	n.96+30085T>C		intron_variant	Intron 1 of 9	2
CXXC4-AS1	ENST00000664466.1	n.212+30085T>C		intron_variant	Intron 1 of 4
CXXC4-AS1	ENST00000723209.1	n.253+30085T>C		intron_variant	Intron 1 of 6

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

African (AFR) AF: 0.207 AC: 8597 AN: 41446

American (AMR) AF: 0.228 AC: 3464 AN: 15208

Ashkenazi Jewish (ASJ) AF: 0.210 AC: 727 AN: 3464

East Asian (EAS) AF: 0.290 AC: 1486 AN: 5124

South Asian (SAS) AF: 0.306 AC: 1467 AN: 4800

European-Finnish (FIN) AF: 0.344 AC: 3640 AN: 10582

Middle Eastern (MID) AF: 0.178 AC: 52 AN: 292

European-Non Finnish (NFE) AF: 0.269 AC: 18264 AN: 67792

Other (OTH) AF: 0.231 AC: 486 AN: 2106

Alfa AF: 0.266 Hom.: 2813

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
PhyloP100		-0.85

Splicing

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

Other links and lift over

dbSNP: rs972583; hg19: chr4-105442302;