rs339078

Variant names:

• chr7-128720943-A-G
• rs339078
• NM_001282788.3:c.687+1860A>G

Your query was ambiguous. Multiple possible variants found:

• chr7-128720943-A-G
• chr7-128720943-A-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

Genes affected

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

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 (EAS) allele frequency at 95% confidence interval = 0.633 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GARIN1B	NM_001282788.3	c.687+1860A>G		intron_variant	Intron 3 of 6	ENST00000621392.5	NP_001269717.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GARIN1B	ENST00000621392.5	c.687+1860A>G		intron_variant	Intron 3 of 6	5	NM_001282788.3	ENSP00000477573.2

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

African (AFR) AF: 0.514 AC: 21279 AN: 41430

American (AMR) AF: 0.568 AC: 8650 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.507 AC: 1761 AN: 3470

East Asian (EAS) AF: 0.652 AC: 3367 AN: 5168

South Asian (SAS) AF: 0.476 AC: 2291 AN: 4814

European-Finnish (FIN) AF: 0.503 AC: 5272 AN: 10490

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.441 AC: 29951 AN: 67918

Other (OTH) AF: 0.464 AC: 978 AN: 2110

Alfa AF: 0.458 Hom.: 19164

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
PhyloP100		-0.68
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: rs339078; hg19: chr7-128360997;