19-50470002-T-C

Variant names:

• chr19-50470002-T-C
• rs1274597
• NM_001308429.2:c.540-2173A>G

Variant summary

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

The NM_001308429.2(GARIN5A):​c.540-2173A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.746 in 152,128 control chromosomes in the GnomAD database, including 43,275 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 0.75 (43275 hom., cov: 32)
• Consequence: GARIN5A NM_001308429.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.334
• Publications: 5 publications found

Genes affected

GARIN5A (HGNC:25107): (golgi associated RAB2 interactor 5A)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.909 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001308429.2. 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
	GARIN5A	NM_001308429.2	MANE Select	c.540-2173A>G		intron	N/A	NP_001295358.1
	GARIN5A	NM_138411.3		c.492-2173A>G		intron	N/A	NP_612420.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GARIN5A	ENST00000600100.6	TSL:1 MANE Select	c.540-2173A>G		intron	N/A	ENSP00000472421.2
	GARIN5A	ENST00000595790.5	TSL:1	c.492-2173A>G		intron	N/A	ENSP00000471272.2
	GARIN5A	ENST00000593796.5	TSL:2	n.162-2270A>G		intron	N/A	ENSP00000471374.1

Frequencies

GnomAD3 genomes AF: 0.746 AC: 113416 AN: 152010 Hom.: 43212 Cov.: 32

Gnomad AFR AF: 0.917

Gnomad AMI AF: 0.773

Gnomad AMR AF: 0.766

Gnomad ASJ AF: 0.659

Gnomad EAS AF: 0.693

Gnomad SAS AF: 0.757

Gnomad FIN AF: 0.652

Gnomad MID AF: 0.737

Gnomad NFE AF: 0.660

Gnomad OTH AF: 0.752

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

GnomAD4 genome AF: 0.746 AC: 113537 AN: 152128 Hom.: 43275 Cov.: 32 AF XY: 0.747 AC XY: 55561 AN XY: 74374

African (AFR) AF: 0.917 AC: 38062 AN: 41508

American (AMR) AF: 0.766 AC: 11711 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.659 AC: 2288 AN: 3472

East Asian (EAS) AF: 0.693 AC: 3582 AN: 5166

South Asian (SAS) AF: 0.758 AC: 3648 AN: 4814

European-Finnish (FIN) AF: 0.652 AC: 6892 AN: 10572

Middle Eastern (MID) AF: 0.735 AC: 216 AN: 294

European-Non Finnish (NFE) AF: 0.660 AC: 44854 AN: 67998

Other (OTH) AF: 0.750 AC: 1579 AN: 2104

Alfa AF: 0.692 Hom.: 68121

Bravo AF: 0.760

Asia WGS AF: 0.745 AC: 2594 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.076
DANN	Benign	0.68
PhyloP100		-0.33
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: rs1274597; hg19: chr19-50973259;