4-5927022-G-C

Variant names:

• chr4-5927022-G-C
• rs10937694
• XM_047415663.1:c.*1965+1389C>G

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The XM_047415663.1(C4orf50):​c.*1965+1389C>G 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: 32)
• Consequence: C4orf50 XM_047415663.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.73

Genes affected

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

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C4orf50	XM_047415663.1	c.*1965+1389C>G		intron_variant	Intron 14 of 14		XP_047271619.1
C4orf50	XM_047415664.1	c.*2674-21573C>G		intron_variant	Intron 12 of 12		XP_047271620.1
C4orf50	XM_047415667.1	c.*2832+1389C>G		intron_variant	Intron 12 of 12		XP_047271623.1
C4orf50	XM_017008893.2	c.*1965+1389C>G		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.*2674-21573C>G		intron_variant	Intron 7 of 7	5		ENSP00000492340.1

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.30
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10937694; hg19: chr4-5928749;