rs6830100

Positions:

• chr4-37528468-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001104629.2(C4orf19):​c.-72-29559G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0824 in 152,182 control chromosomes in the GnomAD database, including 656 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 0.082 (656 hom., cov: 32)
• Consequence: C4orf19 NM_001104629.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.203

Genes affected

C4orf19 (HGNC:25618): (chromosome 4 open reading frame 19) Located in cell junction and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.117 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C4orf19	NM_001104629.2	c.-72-29559G>A		intron_variant		ENST00000381980.9
C4orf19	XM_011513712.3	c.-72-29559G>A		intron_variant
C4orf19	XM_011513713.3	c.-72-29559G>A		intron_variant
C4orf19	XM_047415896.1	c.-72-29559G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C4orf19	ENST00000381980.9	c.-72-29559G>A		intron_variant		1	NM_001104629.2	P1
C4orf19	ENST00000508175.5	c.-72-29559G>A		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.0825 AC: 12541 AN: 152064 Hom.: 653 Cov.: 32

Gnomad AFR AF: 0.0362

Gnomad AMI AF: 0.0384

Gnomad AMR AF: 0.0694

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.00597

Gnomad SAS AF: 0.0834

Gnomad FIN AF: 0.0597

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.119

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.0824 AC: 12539 AN: 152182 Hom.: 656 Cov.: 32 AF XY: 0.0787 AC XY: 5855 AN XY: 74406

Gnomad4 AFR AF: 0.0361

Gnomad4 AMR AF: 0.0693

Gnomad4 ASJ AF: 0.149

Gnomad4 EAS AF: 0.00598

Gnomad4 SAS AF: 0.0836

Gnomad4 FIN AF: 0.0597

Gnomad4 NFE AF: 0.119

Gnomad4 OTH AF: 0.103

Alfa AF: 0.103 Hom.: 147

Bravo AF: 0.0795

Asia WGS AF: 0.0380 AC: 135 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.69
DANN	Benign	0.46

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: rs6830100; hg19: chr4-37530090;