4-5928306-G-T

Variant names:

• chr4-5928306-G-T
• rs4333127
• ENST00000639345.1:n.*2674-22857C>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000639345.1(C4orf50):​n.*2674-22857C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 30)
• Consequence: C4orf50 ENST00000639345.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.679
• Publications: 3 publications found

Genes affected

C4orf50 (HGNC:33766): (chromosome 4 open reading frame 50)

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C4orf50	XM_047415663.1	c.*1965+105C>A		intron_variant	Intron 14 of 14		XP_047271619.1
C4orf50	XM_047415664.1	c.*2674-22857C>A		intron_variant	Intron 12 of 12		XP_047271620.1
C4orf50	XM_047415667.1	c.*2832+105C>A		intron_variant	Intron 12 of 12		XP_047271623.1
C4orf50	XM_017008893.2	c.*1965+105C>A		intron_variant	Intron 12 of 12		XP_016864382.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C4orf50	ENST00000639345.1	n.*2674-22857C>A		intron_variant	Intron 7 of 7	5		ENSP00000492340.1

Frequencies

GnomAD3 genomes Cov.: 30

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

GnomAD4 genome Cov.: 30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.1
DANN	Benign	0.58
PhyloP100		0.68

Splicing

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

Other links and lift over

dbSNP: rs4333127; hg19: chr4-5930033;