chr4-5957408-A-G

Variant names:

• chr4-5957408-A-G
• rs733370
• ENST00000639345.1:n.*1967T>C

Variant summary

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

The ENST00000639345.1(C4orf50):​n.*1967T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.7 in 152,156 control chromosomes in the GnomAD database, including 38,897 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 0.70 (38887 hom., cov: 32)
  • Exomes 𝑓: 0.76 (10 hom.)
• Consequence: C4orf50 ENST00000639345.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.33
• Publications: 6 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.874 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C4orf50	NM_001364690.2	c.*1967T>C		3_prime_UTR_variant	Exon 11 of 11		NP_001351619.1
C4orf50	XM_047415663.1	c.*1100T>C		3_prime_UTR_variant	Exon 13 of 15		XP_047271619.1
C4orf50	XM_047415664.1	c.*1967T>C		3_prime_UTR_variant	Exon 12 of 13		XP_047271620.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C4orf50	ENST00000639345.1	n.*1967T>C		non_coding_transcript_exon_variant	Exon 7 of 8	5		ENSP00000492340.1
C4orf50	ENST00000531445.3	c.*1967T>C		3_prime_UTR_variant	Exon 34 of 34	5		ENSP00000437121.2
C4orf50	ENST00000639345.1	n.*1967T>C		3_prime_UTR_variant	Exon 7 of 8	5		ENSP00000492340.1

Frequencies

GnomAD3 genomes AF: 0.700 AC: 106380 AN: 152004 Hom.: 38821 Cov.: 32

Gnomad AFR AF: 0.882

Gnomad AMI AF: 0.520

Gnomad AMR AF: 0.672

Gnomad ASJ AF: 0.665

Gnomad EAS AF: 0.155

Gnomad SAS AF: 0.541

Gnomad FIN AF: 0.681

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.656

Gnomad OTH AF: 0.681

GnomAD4 exome AF: 0.765 AC: 26 AN: 34 Hom.: 10 Cov.: 0 AF XY: 0.708 AC XY: 17 AN XY: 24

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.800 AC: 8 AN: 10

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.800 AC: 16 AN: 20

Other (OTH) AF: 0.500 AC: 2 AN: 4

GnomAD4 genome AF: 0.700 AC: 106504 AN: 152122 Hom.: 38887 Cov.: 32 AF XY: 0.696 AC XY: 51759 AN XY: 74358

African (AFR) AF: 0.882 AC: 36629 AN: 41534

American (AMR) AF: 0.672 AC: 10274 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.665 AC: 2309 AN: 3472

East Asian (EAS) AF: 0.154 AC: 794 AN: 5144

South Asian (SAS) AF: 0.541 AC: 2610 AN: 4822

European-Finnish (FIN) AF: 0.681 AC: 7211 AN: 10582

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.656 AC: 44596 AN: 67966

Other (OTH) AF: 0.676 AC: 1428 AN: 2112

Alfa AF: 0.668 Hom.: 32039

Bravo AF: 0.701

Asia WGS AF: 0.394 AC: 1369 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.013
DANN	Benign	0.60
PhyloP100		-3.3
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs733370; hg19: chr4-5959135;