NM_001080531.3:c.234-3638C>T

Variant names:

• chr4-145692921-C-T
• rs2132778
• NM_001080531.3:c.234-3638C>T

Variant summary

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

The NM_001080531.3(C4orf51):​c.234-3638C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.47 in 141,478 control chromosomes in the GnomAD database, including 15,304 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 0.47 (15304 hom., cov: 26)
• Consequence: C4orf51 NM_001080531.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.119
• Publications: 4 publications found

Genes affected

C4orf51 (HGNC:37264): (chromosome 4 open reading frame 51)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.567 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001080531.3. 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
	C4orf51	NM_001080531.3	MANE Select	c.234-3638C>T		intron	N/A	NP_001074000.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C4orf51	ENST00000438731.7	TSL:2 MANE Select	c.234-3638C>T		intron	N/A	ENSP00000391404.1

Frequencies

GnomAD3 genomes AF: 0.470 AC: 66463 AN: 141374 Hom.: 15281 Cov.: 26

Gnomad AFR AF: 0.552

Gnomad AMI AF: 0.427

Gnomad AMR AF: 0.578

Gnomad ASJ AF: 0.476

Gnomad EAS AF: 0.455

Gnomad SAS AF: 0.479

Gnomad FIN AF: 0.450

Gnomad MID AF: 0.577

Gnomad NFE AF: 0.401

Gnomad OTH AF: 0.474

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

GnomAD4 genome AF: 0.470 AC: 66533 AN: 141478 Hom.: 15304 Cov.: 26 AF XY: 0.479 AC XY: 32382 AN XY: 67612

African (AFR) AF: 0.552 AC: 21555 AN: 39044

American (AMR) AF: 0.578 AC: 8105 AN: 14028

Ashkenazi Jewish (ASJ) AF: 0.476 AC: 1626 AN: 3414

East Asian (EAS) AF: 0.455 AC: 2071 AN: 4548

South Asian (SAS) AF: 0.479 AC: 2104 AN: 4388

European-Finnish (FIN) AF: 0.450 AC: 3266 AN: 7264

Middle Eastern (MID) AF: 0.579 AC: 147 AN: 254

European-Non Finnish (NFE) AF: 0.401 AC: 26361 AN: 65710

Other (OTH) AF: 0.473 AC: 924 AN: 1952

Alfa AF: 0.418 Hom.: 37151

Bravo AF: 0.463

Asia WGS AF: 0.415 AC: 1440 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	5.7
DANN	Benign	0.71
PhyloP100		-0.12
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: rs2132778; hg19: chr4-146614073;