4-104716137-C-G

Variant names:

• chr4-104716137-C-G
• rs2107005
• ENST00000515127.1:n.407+30503G>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000515127.1(ENSG00000248242):​n.407+30503G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.673 in 151,748 control chromosomes in the GnomAD database, including 37,164 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 0.67 (37164 hom., cov: 31)
• Consequence: ENSG00000248242 ENST00000515127.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.76

Genes affected

ENSG00000248242 (HGNC:):

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.928 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000248242	ENST00000515127.1	n.407+30503G>C		intron_variant	Intron 4 of 5	5
CXXC4-AS1	ENST00000655215.1	n.213-11446C>G		intron_variant	Intron 4 of 5

Frequencies

GnomAD3 genomes AF: 0.673 AC: 102021 AN: 151630 Hom.: 37149 Cov.: 31

Gnomad AFR AF: 0.372

Gnomad AMI AF: 0.769

Gnomad AMR AF: 0.785

Gnomad ASJ AF: 0.693

Gnomad EAS AF: 0.950

Gnomad SAS AF: 0.695

Gnomad FIN AF: 0.827

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.781

Gnomad OTH AF: 0.684

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

GnomAD4 genome AF: 0.673 AC: 102075 AN: 151748 Hom.: 37164 Cov.: 31 AF XY: 0.679 AC XY: 50319 AN XY: 74154

Gnomad4 AFR AF: 0.372

Gnomad4 AMR AF: 0.785

Gnomad4 ASJ AF: 0.693

Gnomad4 EAS AF: 0.950

Gnomad4 SAS AF: 0.695

Gnomad4 FIN AF: 0.827

Gnomad4 NFE AF: 0.781

Gnomad4 OTH AF: 0.686

Alfa AF: 0.656 Hom.: 2428

Bravo AF: 0.660

Asia WGS AF: 0.813 AC: 2822 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.079
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2107005; hg19: chr4-105637294;