chr4-104617315-G-T

Variant names:

• chr4-104617315-G-T
• rs500140
• ENST00000500179.1:n.97-25696G>T

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

The ENST00000500179.1(CXXC4-AS1):​n.97-25696G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00474 in 148,126 control chromosomes in the GnomAD database, including 3 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 0.0047 (3 hom., cov: 30)
• Consequence: CXXC4-AS1 ENST00000500179.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.261

Genes affected

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

LOC124900745 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BS2: High Homozygotes in GnomAd4 at 3 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CXXC4-AS1	NR_125926.1	n.97-25696G>T		intron_variant	Intron 1 of 9
LOC124900745	XR_007058211.1	n.2113+36512C>A		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CXXC4-AS1	ENST00000500179.1	n.97-25696G>T		intron_variant	Intron 1 of 9	2
CXXC4-AS1	ENST00000664466.1	n.213-20583G>T		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.00473 AC: 700 AN: 148034 Hom.: 3 Cov.: 30

Gnomad AFR AF: 0.00131

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00216

Gnomad ASJ AF: 0.00347

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00847

Gnomad FIN AF: 0.00461

Gnomad MID AF: 0.0130

Gnomad NFE AF: 0.00743

Gnomad OTH AF: 0.00744

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

GnomAD4 genome AF: 0.00474 AC: 702 AN: 148126 Hom.: 3 Cov.: 30 AF XY: 0.00485 AC XY: 349 AN XY: 71994

Gnomad4 AFR AF: 0.00131

Gnomad4 AMR AF: 0.00215

Gnomad4 ASJ AF: 0.00347

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00893

Gnomad4 FIN AF: 0.00461

Gnomad4 NFE AF: 0.00743

Gnomad4 OTH AF: 0.00735

Alfa AF: 0.00189 Hom.: 257

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.72
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs500140; hg19: chr4-105538472;