rs16837871

Positions:

• chr4-5939385-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.*1807-10816C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.248 in 152,024 control chromosomes in the GnomAD database, including 6,237 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 0.25 (6237 hom., cov: 32)
• Consequence: C4orf50 XM_017008893.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08

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=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.464 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C4orf50	XM_017008893.2	c.*1807-10816C>T		intron_variant
C4orf50	XM_047415663.1	c.*1807-10816C>T		intron_variant
C4orf50	XM_047415664.1	c.*2673+17317C>T		intron_variant
C4orf50	XM_047415667.1	c.*2674-10816C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C4orf50	ENST00000639345.1	c.*2673+17317C>T		intron_variant, NMD_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.248 AC: 37699 AN: 151908 Hom.: 6225 Cov.: 32

Gnomad AFR AF: 0.470

Gnomad AMI AF: 0.255

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.234

Gnomad EAS AF: 0.0397

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.121

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.178

Gnomad OTH AF: 0.244

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

GnomAD4 genome AF: 0.248 AC: 37743 AN: 152024 Hom.: 6237 Cov.: 32 AF XY: 0.238 AC XY: 17704 AN XY: 74322

Gnomad4 AFR AF: 0.470

Gnomad4 AMR AF: 0.168

Gnomad4 ASJ AF: 0.234

Gnomad4 EAS AF: 0.0396

Gnomad4 SAS AF: 0.106

Gnomad4 FIN AF: 0.121

Gnomad4 NFE AF: 0.178

Gnomad4 OTH AF: 0.241

Alfa AF: 0.206 Hom.: 1053

Bravo AF: 0.263

Asia WGS AF: 0.115 AC: 404 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.19
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16837871; hg19: chr4-5941112; COSMIC: COSV66488655;