rs10937694

chr4-5927022-G-Achr4-5927022-G-C

Variant summary

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

The XM_017008893.2(C4orf50):c.*1965+1389C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.356 in 152,078 control chromosomes in the GnomAD database, including 9,863 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 0.36 (9863 hom., cov: 32)
• Consequence: C4orf50 XM_017008893.2 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 Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.368 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C4orf50	XM_017008893.2	c.*1965+1389C>T		intron_variant
C4orf50	XM_047415663.1	c.*1965+1389C>T		intron_variant
C4orf50	XM_047415664.1	c.*2674-21573C>T		intron_variant
C4orf50	XM_047415667.1	c.*2832+1389C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C4orf50	ENST00000639345.1	c.*2674-21573C>T		intron_variant, NMD_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.356 AC: 54079 AN: 151960 Hom.: 9849 Cov.: 32

Gnomad AFR AF: 0.356

Gnomad AMI AF: 0.362

Gnomad AMR AF: 0.354

Gnomad ASJ AF: 0.413

Gnomad EAS AF: 0.0711

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.411

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.372

Gnomad OTH AF: 0.337

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

GnomAD4 genome AF: 0.356 AC: 54136 AN: 152078 Hom.: 9863 Cov.: 32 AF XY: 0.358 AC XY: 26578 AN XY: 74334

Gnomad4 AFR AF: 0.356

Gnomad4 AMR AF: 0.354

Gnomad4 ASJ AF: 0.413

Gnomad4 EAS AF: 0.0715

Gnomad4 SAS AF: 0.295

Gnomad4 FIN AF: 0.411

Gnomad4 NFE AF: 0.372

Gnomad4 OTH AF: 0.339

Alfa AF: 0.324 Hom.: 2494

Bravo AF: 0.349

Asia WGS AF: 0.199 AC: 695 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.47
Dann	Benign	0.34

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;