NM_001364689.3:c.3267C>T

Variant names:

• chr4-5988779-G-A
• rs148575061
• NM_001364689.3:c.3267C>T

Variant summary

Our verdict is Benign. The variant received -11 ACMG points: 0P and 11B. BP4_Strong BP6_Moderate BP7 BS2

The NM_001364689.3(C4orf50):​c.3267C>T​(p.Asn1089Asn) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00309 in 1,536,058 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0021 (1 hom., cov: 32)
  • Exomes 𝑓: 0.0032 (6 hom.)
• Consequence: C4orf50 NM_001364689.3 synonymous
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.13
• Publications: 1 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -11 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BP6: Variant 4-5988779-G-A is Benign according to our data. Variant chr4-5988779-G-A is described in ClinVar as Likely_benign. ClinVar VariationId is 2654615.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=-1.13 with no splicing effect.
• BS2: High Homozygotes in GnomAdExome4 at 6 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001364689.3. 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
	C4orf50	NM_001364689.3	MANE Select	c.3267C>T	p.Asn1089Asn	synonymous	Exon 6 of 12	NP_001351618.1	Q6ZRC1
	C4orf50	NM_001364690.2		c.2730C>T	p.Asn910Asn	synonymous	Exon 5 of 11	NP_001351619.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C4orf50	ENST00000711657.1	MANE Select	c.3267C>T	p.Asn1089Asn	synonymous	Exon 6 of 12	ENSP00000518823.1	Q6ZRC1
	C4orf50	ENST00000531445.3	TSL:5	c.3267C>T	p.Asn1089Asn	synonymous	Exon 28 of 34	ENSP00000437121.2	Q6ZRC1
	C4orf50	ENST00000639345.1	TSL:5	n.1284C>T		non_coding_transcript_exon	Exon 1 of 8	ENSP00000492340.1	A0A1W2PRI9

Frequencies

GnomAD3 genomes AF: 0.00210 AC: 319 AN: 152114 Hom.: 1 Cov.: 32

Gnomad AFR AF: 0.00101

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00203

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.000414

Gnomad FIN AF: 0.000850

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00338

Gnomad OTH AF: 0.00192

GnomAD2 exomes AF: 0.00178 AC: 240 AN: 134626 AF XY: 0.00170

Gnomad AFR exome AF: 0.000620

Gnomad AMR exome AF: 0.000858

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.0000952

Gnomad FIN exome AF: 0.00111

Gnomad NFE exome AF: 0.00369

Gnomad OTH exome AF: 0.00169

GnomAD4 exome AF: 0.00320 AC: 4428 AN: 1383826 Hom.: 6 Cov.: 82 AF XY: 0.00308 AC XY: 2106 AN XY: 682854

African (AFR) AF: 0.000791 AC: 25 AN: 31594

American (AMR) AF: 0.00109 AC: 39 AN: 35700

Ashkenazi Jewish (ASJ) AF: 0.000159 AC: 4 AN: 25182

East Asian (EAS) AF: 0.0000280 AC: 1 AN: 35734

South Asian (SAS) AF: 0.000164 AC: 13 AN: 79236

European-Finnish (FIN) AF: 0.000944 AC: 32 AN: 33898

Middle Eastern (MID) AF: 0.000176 AC: 1 AN: 5696

European-Non Finnish (NFE) AF: 0.00386 AC: 4160 AN: 1078880

Other (OTH) AF: 0.00264 AC: 153 AN: 57906

GnomAD4 genome AF: 0.00210 AC: 319 AN: 152232 Hom.: 1 Cov.: 32 AF XY: 0.00183 AC XY: 136 AN XY: 74422

African (AFR) AF: 0.00101 AC: 42 AN: 41534

American (AMR) AF: 0.00203 AC: 31 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3472

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5172

South Asian (SAS) AF: 0.000415 AC: 2 AN: 4822

European-Finnish (FIN) AF: 0.000850 AC: 9 AN: 10594

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.00338 AC: 230 AN: 68032

Other (OTH) AF: 0.00190 AC: 4 AN: 2108

Alfa AF: 0.00110 Hom.: 0

Bravo AF: 0.00212

ClinVar

ClinVar submissions

Significance: Likely benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.062
DANN	Benign	0.55
PhyloP100		-1.1
Mutation Taster		=100/0	polymorphism

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: rs148575061; hg19: chr4-5990506; COSMIC: COSV100136277;