rs733370

Positions:

• chr4-5957408-A-G

Variant summary

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

The XM_017008893.2(C4orf50):​c.*1100T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.7 in 152,156 control chromosomes in the GnomAD database, including 38,897 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 0.70 (38887 hom., cov: 32)
  • Exomes 𝑓: 0.76 (10 hom.)
• Consequence: C4orf50 XM_017008893.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.33

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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.874 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
C4orf50	XM_017008893.2	c.*1100T>C		3_prime_UTR_variant	11/13		XP_016864382.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
C4orf50	ENST00000531445.3	c.*1967T>C		3_prime_UTR_variant	34/34	5		ENSP00000437121	P1
C4orf50	ENST00000639345.1	c.*1967T>C		3_prime_UTR_variant, NMD_transcript_variant	7/8	5		ENSP00000492340

Frequencies

GnomAD3 genomes AF: 0.700 AC: 106380 AN: 152004 Hom.: 38821 Cov.: 32

Gnomad AFR AF: 0.882

Gnomad AMI AF: 0.520

Gnomad AMR AF: 0.672

Gnomad ASJ AF: 0.665

Gnomad EAS AF: 0.155

Gnomad SAS AF: 0.541

Gnomad FIN AF: 0.681

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.656

Gnomad OTH AF: 0.681

GnomAD4 exome AF: 0.765 AC: 26 AN: 34 Hom.: 10 Cov.: 0 AF XY: 0.708 AC XY: 17 AN XY: 24

Gnomad4 FIN exome AF: 0.800

Gnomad4 NFE exome AF: 0.800

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.700 AC: 106504 AN: 152122 Hom.: 38887 Cov.: 32 AF XY: 0.696 AC XY: 51759 AN XY: 74358

Gnomad4 AFR AF: 0.882

Gnomad4 AMR AF: 0.672

Gnomad4 ASJ AF: 0.665

Gnomad4 EAS AF: 0.154

Gnomad4 SAS AF: 0.541

Gnomad4 FIN AF: 0.681

Gnomad4 NFE AF: 0.656

Gnomad4 OTH AF: 0.676

Alfa AF: 0.666 Hom.: 27346

Bravo AF: 0.701

Asia WGS AF: 0.394 AC: 1369 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.013
DANN	Benign	0.60

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs733370; hg19: chr4-5959135;