rs10937694

Variant names:

• chr4-5927022-G-A
• rs10937694
• XM_047415663.1:c.*1965+1389C>T

Your query was ambiguous. Multiple possible variants found:

• chr4-5927022-G-A
• chr4-5927022-G-C

Variant summary

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

The XM_047415663.1(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_047415663.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.73
• Publications: 0 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=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.368 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C4orf50	ENST00000639345.1	TSL:5	n.*2674-21573C>T		intron	N/A	ENSP00000492340.1

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

African (AFR) AF: 0.356 AC: 14757 AN: 41482

American (AMR) AF: 0.354 AC: 5415 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.413 AC: 1431 AN: 3466

East Asian (EAS) AF: 0.0715 AC: 370 AN: 5178

South Asian (SAS) AF: 0.295 AC: 1420 AN: 4812

European-Finnish (FIN) AF: 0.411 AC: 4341 AN: 10568

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.372 AC: 25258 AN: 67964

Other (OTH) AF: 0.339 AC: 715 AN: 2112

Alfa AF: 0.326 Hom.: 2788

Bravo AF: 0.349

Asia WGS AF: 0.199 AC: 695 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.47
DANN	Benign	0.34
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs10937694; hg19: chr4-5928749;