14-67215919-C-A

Position:

• chr14-67215919-C-A

Variant summary

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

The NM_001395907.1(GARIN2):​c.1161-5860C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.148 in 152,090 control chromosomes in the GnomAD database, including 3,122 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 0.15 (3122 hom., cov: 32)
• Consequence: GARIN2 NM_001395907.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.56

Genes affected

GARIN2 (HGNC:20101): (golgi associated RAB2 interactor family member 2)

GPHN (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.406 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GARIN2	NM_001395907.1	c.1161-5860C>A		intron_variant		ENST00000696955.1	NP_001382836.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GARIN2	ENST00000696955.1	c.1161-5860C>A		intron_variant			NM_001395907.1	ENSP00000512992	P2

Frequencies

GnomAD3 genomes AF: 0.148 AC: 22487 AN: 151972 Hom.: 3115 Cov.: 32

Gnomad AFR AF: 0.310

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.0666

Gnomad EAS AF: 0.421

Gnomad SAS AF: 0.260

Gnomad FIN AF: 0.0538

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0267

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.148 AC: 22529 AN: 152090 Hom.: 3122 Cov.: 32 AF XY: 0.155 AC XY: 11491 AN XY: 74360

Gnomad4 AFR AF: 0.310

Gnomad4 AMR AF: 0.215

Gnomad4 ASJ AF: 0.0666

Gnomad4 EAS AF: 0.421

Gnomad4 SAS AF: 0.260

Gnomad4 FIN AF: 0.0538

Gnomad4 NFE AF: 0.0267

Gnomad4 OTH AF: 0.148

Alfa AF: 0.0878 Hom.: 239

Bravo AF: 0.167

Asia WGS AF: 0.292 AC: 1020 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	0.25
DANN	Benign	0.63

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: rs10431718; hg19: chr14-67682636;