4-145692921-C-T

Position:

• chr4-145692921-C-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
C4orf51	NM_001080531.3	c.234-3638C>T		intron_variant		ENST00000438731.7	NP_001074000.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
C4orf51	ENST00000438731.7	c.234-3638C>T		intron_variant		2	NM_001080531.3	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

Gnomad4 AFR AF: 0.552

Gnomad4 AMR AF: 0.578

Gnomad4 ASJ AF: 0.476

Gnomad4 EAS AF: 0.455

Gnomad4 SAS AF: 0.479

Gnomad4 FIN AF: 0.450

Gnomad4 NFE AF: 0.401

Gnomad4 OTH AF: 0.473

Alfa AF: 0.409 Hom.: 21227

Bravo AF: 0.463

Asia WGS AF: 0.415 AC: 1440 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	5.7
DANN	Benign	0.71

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

Publications

LitVar

Other links and lift over

dbSNP: rs2132778; hg19: chr4-146614073;