7-128720943-A-T

Variant names:

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

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_032599.4(GARIN1B):​c.687+1860A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
• Consequence: GARIN1B NM_032599.4 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032599.4. 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
	GARIN1B	NM_001282788.3	MANE Select	c.687+1860A>T		intron	N/A	NP_001269717.1
	GARIN1B	NM_032599.4		c.687+1860A>T		intron	N/A	NP_115988.1
	GARIN1B	NM_001282789.2		c.390+1860A>T		intron	N/A	NP_001269718.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GARIN1B	ENST00000621392.5	TSL:5 MANE Select	c.687+1860A>T		intron	N/A	ENSP00000477573.2
	GARIN1B	ENST00000315184.9	TSL:1	c.687+1860A>T		intron	N/A	ENSP00000326652.4
	GARIN1B	ENST00000471558.5	TSL:1	n.687+1860A>T		intron	N/A	ENSP00000418672.1

Frequencies

GnomAD3 genomes Cov.: 31

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

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	7.8
DANN	Benign	0.91
PhyloP100		-0.68

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;