rs339078

chr7-128720943-A-Gchr7-128720943-A-T

Variant summary

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

The NM_001282788.3(GARIN1B):c.687+1860A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.487 in 151,834 control chromosomes in the GnomAD database, including 18,314 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 0.49 (18314 hom., cov: 31)
• Consequence: GARIN1B NM_001282788.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.682

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=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.633 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GARIN1B	NM_001282788.3	c.687+1860A>G		intron_variant		ENST00000621392.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GARIN1B	ENST00000621392.5	c.687+1860A>G		intron_variant		5	NM_001282788.3	A1

Frequencies

GnomAD3 genomes AF: 0.487 AC: 73809 AN: 151714 Hom.: 18285 Cov.: 31

Gnomad AFR AF: 0.513

Gnomad AMI AF: 0.263

Gnomad AMR AF: 0.567

Gnomad ASJ AF: 0.507

Gnomad EAS AF: 0.651

Gnomad SAS AF: 0.477

Gnomad FIN AF: 0.503

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.441

Gnomad OTH AF: 0.464

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

GnomAD4 genome AF: 0.487 AC: 73894 AN: 151834 Hom.: 18314 Cov.: 31 AF XY: 0.492 AC XY: 36504 AN XY: 74164

Gnomad4 AFR AF: 0.514

Gnomad4 AMR AF: 0.568

Gnomad4 ASJ AF: 0.507

Gnomad4 EAS AF: 0.652

Gnomad4 SAS AF: 0.476

Gnomad4 FIN AF: 0.503

Gnomad4 NFE AF: 0.441

Gnomad4 OTH AF: 0.464

Alfa AF: 0.457 Hom.: 15975

Bravo AF: 0.495

Asia WGS AF: 0.550 AC: 1907 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	8.1
Dann	Benign	0.94

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: rs339078; hg19: chr7-128360997;