rs339093

Positions:

• chr7-128716494-T-C

Variant summary

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

The NM_001282788.3(GARIN1B):​c.250-319T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.157 in 152,140 control chromosomes in the GnomAD database, including 2,267 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 0.16 (2267 hom., cov: 32)
• Consequence: GARIN1B NM_001282788.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.472

Genes affected

GARIN1B (HGNC:30704): (golgi associated RAB2 interactor 1B)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.256 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GARIN1B	NM_001282788.3	c.250-319T>C		intron_variant		ENST00000621392.5	NP_001269717.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GARIN1B	ENST00000621392.5	c.250-319T>C		intron_variant		5	NM_001282788.3	ENSP00000477573	A1

Frequencies

GnomAD3 genomes AF: 0.157 AC: 23836 AN: 152022 Hom.: 2264 Cov.: 32

Gnomad AFR AF: 0.260

Gnomad AMI AF: 0.0789

Gnomad AMR AF: 0.0892

Gnomad ASJ AF: 0.0695

Gnomad EAS AF: 0.0286

Gnomad SAS AF: 0.0919

Gnomad FIN AF: 0.165

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.157 AC: 23862 AN: 152140 Hom.: 2267 Cov.: 32 AF XY: 0.156 AC XY: 11598 AN XY: 74392

Gnomad4 AFR AF: 0.260

Gnomad4 AMR AF: 0.0890

Gnomad4 ASJ AF: 0.0695

Gnomad4 EAS AF: 0.0283

Gnomad4 SAS AF: 0.0920

Gnomad4 FIN AF: 0.165

Gnomad4 NFE AF: 0.129

Gnomad4 OTH AF: 0.130

Alfa AF: 0.138 Hom.: 328

Bravo AF: 0.154

Asia WGS AF: 0.0590 AC: 204 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.2
DANN	Benign	0.66

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: rs339093; hg19: chr7-128356548;