rs726111

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C4orf50	XM_047415663.1	c.*1966-4807C>T		intron_variant	Intron 14 of 14		XP_047271619.1
C4orf50	XM_047415664.1	c.*2674-4807C>T		intron_variant	Intron 12 of 12		XP_047271620.1
C4orf50	XM_047415667.1	c.*2833-4807C>T		intron_variant	Intron 12 of 12		XP_047271623.1
C4orf50	XM_017008893.2	c.*1966-4807C>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.*2674-4807C>T		intron_variant	Intron 7 of 7	5		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 v4.3

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;