chr4-5910256-G-A

Variant names:

• chr4-5910256-G-A
• rs726111
• ENST00000639345.1:n.*2674-4807C>T

Variant summary

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

The ENST00000639345.1(C4orf50):​n.*2674-4807C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.386 in 152,028 control chromosomes in the GnomAD database, including 14,040 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 0.39 (14040 hom., cov: 32)
• Consequence: C4orf50 ENST00000639345.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.235
• Publications: 4 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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.718 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000639345.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C4orf50	ENST00000639345.1	TSL:5	n.*2674-4807C>T		intron	N/A	ENSP00000492340.1

Frequencies

GnomAD3 genomes AF: 0.386 AC: 58620 AN: 151910 Hom.: 14047 Cov.: 32

Gnomad AFR AF: 0.0949

Gnomad AMI AF: 0.561

Gnomad AMR AF: 0.408

Gnomad ASJ AF: 0.469

Gnomad EAS AF: 0.739

Gnomad SAS AF: 0.510

Gnomad FIN AF: 0.509

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.496

Gnomad OTH AF: 0.396

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

GnomAD4 genome AF: 0.386 AC: 58611 AN: 152028 Hom.: 14040 Cov.: 32 AF XY: 0.389 AC XY: 28903 AN XY: 74298

African (AFR) AF: 0.0946 AC: 3928 AN: 41512

American (AMR) AF: 0.409 AC: 6241 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.469 AC: 1624 AN: 3464

East Asian (EAS) AF: 0.738 AC: 3811 AN: 5166

South Asian (SAS) AF: 0.509 AC: 2450 AN: 4816

European-Finnish (FIN) AF: 0.509 AC: 5366 AN: 10540

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.496 AC: 33713 AN: 67938

Other (OTH) AF: 0.397 AC: 837 AN: 2110

Alfa AF: 0.462 Hom.: 8981

Bravo AF: 0.365

Asia WGS AF: 0.578 AC: 2011 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.2
DANN	Benign	0.67
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs726111; hg19: chr4-5911983;