4-5910256-G-A

Position:

• chr4-5910256-G-A

Variant summary

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

The XM_017008893.2(C4orf50):​c.*1966-4807C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.386 in 152,028 control chromosomes in the GnomAD database, including 14,040 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 0.39 (14040 hom., cov: 32)
• Consequence: C4orf50 XM_017008893.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.235

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.718 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C4orf50	XM_017008893.2	c.*1966-4807C>T		intron_variant
C4orf50	XM_047415663.1	c.*1966-4807C>T		intron_variant
C4orf50	XM_047415664.1	c.*2674-4807C>T		intron_variant
C4orf50	XM_047415667.1	c.*2833-4807C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C4orf50	ENST00000639345.1	c.*2674-4807C>T		intron_variant, NMD_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.386 AC: 58620 AN: 151910 Hom.: 14047 Cov.: 32

Gnomad AFR AF: 0.0949

Gnomad AMI AF: 0.561

Gnomad AMR AF: 0.408

Gnomad ASJ AF: 0.469

Gnomad EAS AF: 0.739

Gnomad SAS AF: 0.510

Gnomad FIN AF: 0.509

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.496

Gnomad OTH AF: 0.396

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

GnomAD4 genome AF: 0.386 AC: 58611 AN: 152028 Hom.: 14040 Cov.: 32 AF XY: 0.389 AC XY: 28903 AN XY: 74298

Gnomad4 AFR AF: 0.0946

Gnomad4 AMR AF: 0.409

Gnomad4 ASJ AF: 0.469

Gnomad4 EAS AF: 0.738

Gnomad4 SAS AF: 0.509

Gnomad4 FIN AF: 0.509

Gnomad4 NFE AF: 0.496

Gnomad4 OTH AF: 0.397

Alfa AF: 0.466 Hom.: 8123

Bravo AF: 0.365

Asia WGS AF: 0.578 AC: 2011 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.2
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs726111; hg19: chr4-5911983;