7-128716494-T-C

Variant names:

• chr7-128716494-T-C
• rs339093
• NM_001282788.3:c.250-319T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.256 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001282788.3. 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.250-319T>C		intron	N/A	NP_001269717.1
	GARIN1B	NM_032599.4		c.250-319T>C		intron	N/A	NP_115988.1
	GARIN1B	NM_001282789.2		c.14-319T>C		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.250-319T>C		intron	N/A	ENSP00000477573.2
	GARIN1B	ENST00000315184.9	TSL:1	c.250-319T>C		intron	N/A	ENSP00000326652.4
	GARIN1B	ENST00000471558.5	TSL:1	n.250-319T>C		intron	N/A	ENSP00000418672.1

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

African (AFR) AF: 0.260 AC: 10792 AN: 41456

American (AMR) AF: 0.0890 AC: 1361 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0695 AC: 241 AN: 3466

East Asian (EAS) AF: 0.0283 AC: 147 AN: 5190

South Asian (SAS) AF: 0.0920 AC: 444 AN: 4826

European-Finnish (FIN) AF: 0.165 AC: 1754 AN: 10602

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.129 AC: 8759 AN: 67996

Other (OTH) AF: 0.130 AC: 275 AN: 2112

Alfa AF: 0.141 Hom.: 362

Bravo AF: 0.154

Asia WGS AF: 0.0590 AC: 204 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.2
DANN	Benign	0.66
PhyloP100		-0.47
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: rs339093; hg19: chr7-128356548;