rs9684740

Positions:

• chr4-5947066-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.*1806+9636C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.33 in 152,050 control chromosomes in the GnomAD database, including 8,692 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 0.33 (8692 hom., cov: 33)
• Consequence: C4orf50 XM_017008893.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20

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=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.369 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C4orf50	XM_017008893.2	c.*1806+9636C>T		intron_variant
C4orf50	XM_047415663.1	c.*1806+9636C>T		intron_variant
C4orf50	XM_047415664.1	c.*2673+9636C>T		intron_variant
C4orf50	XM_047415667.1	c.*2673+9636C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C4orf50	ENST00000639345.1	c.*2673+9636C>T		intron_variant, NMD_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.330 AC: 50152 AN: 151932 Hom.: 8689 Cov.: 33

Gnomad AFR AF: 0.314

Gnomad AMI AF: 0.422

Gnomad AMR AF: 0.225

Gnomad ASJ AF: 0.330

Gnomad EAS AF: 0.0618

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.410

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.373

Gnomad OTH AF: 0.313

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

GnomAD4 genome AF: 0.330 AC: 50174 AN: 152050 Hom.: 8692 Cov.: 33 AF XY: 0.328 AC XY: 24376 AN XY: 74306

Gnomad4 AFR AF: 0.314

Gnomad4 AMR AF: 0.224

Gnomad4 ASJ AF: 0.330

Gnomad4 EAS AF: 0.0616

Gnomad4 SAS AF: 0.310

Gnomad4 FIN AF: 0.410

Gnomad4 NFE AF: 0.373

Gnomad4 OTH AF: 0.309

Alfa AF: 0.353 Hom.: 16465

Bravo AF: 0.311

Asia WGS AF: 0.188 AC: 652 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.4
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9684740; hg19: chr4-5948793;