rs4333127

Variant names:

• chr4-5928306-G-A
• rs4333127
• ENST00000639345.1:n.*2674-22857C>T

Your query was ambiguous. Multiple possible variants found:

• chr4-5928306-G-A
• chr4-5928306-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000639345.1(C4orf50):​n.*2674-22857C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.913 in 152,040 control chromosomes in the GnomAD database, including 63,458 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 0.91 (63458 hom., cov: 30)
• Consequence: C4orf50 ENST00000639345.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.679
• Publications: 3 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.936 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C4orf50	XM_047415663.1	c.*1965+105C>T		intron_variant	Intron 14 of 14		XP_047271619.1
C4orf50	XM_047415664.1	c.*2674-22857C>T		intron_variant	Intron 12 of 12		XP_047271620.1
C4orf50	XM_047415667.1	c.*2832+105C>T		intron_variant	Intron 12 of 12		XP_047271623.1
C4orf50	XM_017008893.2	c.*1965+105C>T		intron_variant	Intron 12 of 12		XP_016864382.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C4orf50	ENST00000639345.1	n.*2674-22857C>T		intron_variant	Intron 7 of 7	5		ENSP00000492340.1

Frequencies

GnomAD3 genomes AF: 0.913 AC: 138718 AN: 151922 Hom.: 63410 Cov.: 30

Gnomad AFR AF: 0.944

Gnomad AMI AF: 0.858

Gnomad AMR AF: 0.861

Gnomad ASJ AF: 0.908

Gnomad EAS AF: 0.885

Gnomad SAS AF: 0.934

Gnomad FIN AF: 0.937

Gnomad MID AF: 0.943

Gnomad NFE AF: 0.904

Gnomad OTH AF: 0.903

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

GnomAD4 genome AF: 0.913 AC: 138823 AN: 152040 Hom.: 63458 Cov.: 30 AF XY: 0.915 AC XY: 67994 AN XY: 74312

African (AFR) AF: 0.944 AC: 39107 AN: 41438

American (AMR) AF: 0.861 AC: 13146 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.908 AC: 3153 AN: 3472

East Asian (EAS) AF: 0.884 AC: 4569 AN: 5166

South Asian (SAS) AF: 0.934 AC: 4491 AN: 4808

European-Finnish (FIN) AF: 0.937 AC: 9902 AN: 10566

Middle Eastern (MID) AF: 0.956 AC: 281 AN: 294

European-Non Finnish (NFE) AF: 0.904 AC: 61489 AN: 68010

Other (OTH) AF: 0.903 AC: 1904 AN: 2108

Alfa AF: 0.912 Hom.: 20290

Bravo AF: 0.906

Asia WGS AF: 0.910 AC: 3167 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.4
DANN	Benign	0.51
PhyloP100		0.68

Splicing

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

Other links and lift over

dbSNP: rs4333127; hg19: chr4-5930033;