chr4-37528468-G-A

Variant names:

• chr4-37528468-G-A
• rs6830100
• NM_001104629.2:c.-72-29559G>A

Variant summary

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

The NM_001104629.2(PGCKA1):​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: PGCKA1 NM_001104629.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.203
• Publications: 0 publications found

Genes affected

PGCKA1 (HGNC:25618): (chromosome 4 open reading frame 19) Located in cell junction and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001104629.2. 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
	PGCKA1	NM_001104629.2	MANE Select	c.-72-29559G>A		intron	N/A	NP_001098099.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C4orf19	ENST00000381980.9	TSL:1 MANE Select	c.-72-29559G>A		intron	N/A	ENSP00000371408.4
	C4orf19	ENST00000508175.5	TSL:3	c.-72-29559G>A		intron	N/A	ENSP00000421537.1

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

African (AFR) AF: 0.0361 AC: 1499 AN: 41534

American (AMR) AF: 0.0693 AC: 1060 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.149 AC: 516 AN: 3472

East Asian (EAS) AF: 0.00598 AC: 31 AN: 5180

South Asian (SAS) AF: 0.0836 AC: 403 AN: 4818

European-Finnish (FIN) AF: 0.0597 AC: 632 AN: 10588

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.119 AC: 8104 AN: 67990

Other (OTH) AF: 0.103 AC: 218 AN: 2108

Alfa AF: 0.101 Hom.: 147

Bravo AF: 0.0795

Asia WGS AF: 0.0380 AC: 135 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.69
DANN	Benign	0.46
PhyloP100		-0.20
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: rs6830100; hg19: chr4-37530090;