chr4-104617315-G-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

Genes affected

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

ENSG00000248242 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

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

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

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

Ensembl Transcripts

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

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

African (AFR) AF: 0.00131 AC: 52 AN: 39816

American (AMR) AF: 0.00215 AC: 32 AN: 14858

Ashkenazi Jewish (ASJ) AF: 0.00347 AC: 12 AN: 3456

East Asian (EAS) AF: 0.00 AC: 0 AN: 5060

South Asian (SAS) AF: 0.00893 AC: 42 AN: 4702

European-Finnish (FIN) AF: 0.00461 AC: 44 AN: 9540

Middle Eastern (MID) AF: 0.0141 AC: 4 AN: 284

European-Non Finnish (NFE) AF: 0.00743 AC: 501 AN: 67462

Other (OTH) AF: 0.00735 AC: 15 AN: 2040

Alfa AF: 0.00179 Hom.: 263

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.72
DANN	Benign	0.51
PhyloP100		-0.26
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs500140; hg19: chr4-105538472;