4-104617315-G-A

Variant names:

• chr4-104617315-G-A
• rs500140
• ENST00000500179.1:n.97-25696G>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.97-25696G>A variant causes a intron 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 ENST00000500179.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.261
• Publications: 1 publications found

Genes affected

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

ENSG00000248242 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000500179.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CXXC4-AS1	NR_125926.1		n.97-25696G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CXXC4-AS1	ENST00000500179.1	TSL:2	n.97-25696G>A		intron	N/A
	CXXC4-AS1	ENST00000664466.1		n.213-20583G>A		intron	N/A
	ENSG00000248242	ENST00000723032.1		n.428+36512C>T		intron	N/A

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

African (AFR) AF: 0.177 AC: 7039 AN: 39792

American (AMR) AF: 0.283 AC: 4202 AN: 14844

Ashkenazi Jewish (ASJ) AF: 0.258 AC: 891 AN: 3456

East Asian (EAS) AF: 0.272 AC: 1377 AN: 5054

South Asian (SAS) AF: 0.122 AC: 573 AN: 4698

European-Finnish (FIN) AF: 0.270 AC: 2574 AN: 9532

Middle Eastern (MID) AF: 0.222 AC: 63 AN: 284

European-Non Finnish (NFE) AF: 0.272 AC: 18362 AN: 67410

Other (OTH) AF: 0.261 AC: 532 AN: 2040

Alfa AF: 0.134 Hom.: 263

Bravo AF: 0.240

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.4
DANN	Benign	0.59
PhyloP100		-0.26

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs500140;

hg19: chr4-105538472;