rs6971091

Variant names:

• chr7-128723233-G-A
• rs6971091
• NM_001282788.3:c.724G>A

Your query was ambiguous. Multiple possible variants found:

• chr7-128723233-G-A
• chr7-128723233-G-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.724G>A​(p.Glu242Lys) variant causes a missense change. The variant allele was found at a frequency of 0.218 in 1,611,952 control chromosomes in the GnomAD database, including 40,350 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 0.18 (2823 hom., cov: 31)
  • Exomes 𝑓: 0.22 (37527 hom.)
• Consequence: GARIN1B NM_001282788.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.07
• Publications: 36 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 (MetaRNN=0.0016109645).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.263 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GARIN1B	NM_001282788.3	MANE Select	c.724G>A	p.Glu242Lys	missense	Exon 4 of 7	NP_001269717.1	Q96KD3-2
	GARIN1B	NM_032599.4		c.724G>A	p.Glu242Lys	missense	Exon 4 of 7	NP_115988.1	Q96KD3-1
	GARIN1B	NM_001282789.2		c.427G>A	p.Glu143Lys	missense	Exon 5 of 8	NP_001269718.1	Q96KD3-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GARIN1B	ENST00000621392.5	TSL:5 MANE Select	c.724G>A	p.Glu242Lys	missense	Exon 4 of 7	ENSP00000477573.2	Q96KD3-2
	GARIN1B	ENST00000315184.9	TSL:1	c.724G>A	p.Glu242Lys	missense	Exon 4 of 7	ENSP00000326652.4	Q96KD3-1
	GARIN1B	ENST00000471558.5	TSL:1	n.724G>A		non_coding_transcript_exon	Exon 4 of 6	ENSP00000418672.1	F8WC62

Frequencies

GnomAD3 genomes AF: 0.181 AC: 27537 AN: 151920 Hom.: 2822 Cov.: 31

Gnomad AFR AF: 0.0835

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.189

Gnomad EAS AF: 0.113

Gnomad SAS AF: 0.274

Gnomad FIN AF: 0.246

Gnomad MID AF: 0.204

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.186

GnomAD2 exomes AF: 0.202 AC: 50665 AN: 251332 AF XY: 0.210

Gnomad AFR exome AF: 0.0794

Gnomad AMR exome AF: 0.116

Gnomad ASJ exome AF: 0.188

Gnomad EAS exome AF: 0.113

Gnomad FIN exome AF: 0.239

Gnomad NFE exome AF: 0.231

Gnomad OTH exome AF: 0.192

GnomAD4 exome AF: 0.222 AC: 323988 AN: 1459914 Hom.: 37527 Cov.: 32 AF XY: 0.225 AC XY: 163056 AN XY: 726268

African (AFR) AF: 0.0797 AC: 2665 AN: 33434

American (AMR) AF: 0.120 AC: 5361 AN: 44664

Ashkenazi Jewish (ASJ) AF: 0.187 AC: 4884 AN: 26084

East Asian (EAS) AF: 0.122 AC: 4830 AN: 39638

South Asian (SAS) AF: 0.286 AC: 24661 AN: 86174

European-Finnish (FIN) AF: 0.238 AC: 12681 AN: 53254

Middle Eastern (MID) AF: 0.196 AC: 1126 AN: 5744

European-Non Finnish (NFE) AF: 0.230 AC: 254998 AN: 1110648

Other (OTH) AF: 0.212 AC: 12782 AN: 60274

GnomAD4 genome AF: 0.181 AC: 27542 AN: 152038 Hom.: 2823 Cov.: 31 AF XY: 0.183 AC XY: 13587 AN XY: 74298

African (AFR) AF: 0.0833 AC: 3457 AN: 41486

American (AMR) AF: 0.171 AC: 2606 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.189 AC: 656 AN: 3462

East Asian (EAS) AF: 0.113 AC: 583 AN: 5172

South Asian (SAS) AF: 0.276 AC: 1327 AN: 4816

European-Finnish (FIN) AF: 0.246 AC: 2602 AN: 10558

Middle Eastern (MID) AF: 0.202 AC: 59 AN: 292

European-Non Finnish (NFE) AF: 0.231 AC: 15726 AN: 67964

Other (OTH) AF: 0.189 AC: 397 AN: 2100

Alfa AF: 0.212 Hom.: 16120

Bravo AF: 0.163

TwinsUK AF: 0.232 AC: 859

ALSPAC AF: 0.219 AC: 844

ESP6500AA AF: 0.0797 AC: 351

ESP6500EA AF: 0.229 AC: 1973

ExAC AF: 0.204 AC: 24748

Asia WGS AF: 0.202 AC: 703 AN: 3478

EpiCase AF: 0.225

EpiControl AF: 0.218

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.094
BayesDel_addAF	Benign	-0.58	T
BayesDel_noAF	Benign	-0.46
CADD	Uncertain	24
DANN	Uncertain	1.0
DEOGEN2	Benign	0.0094	T
Eigen	Uncertain	0.52
Eigen_PC	Uncertain	0.54
FATHMM_MKL	Uncertain	0.87	D
LIST_S2	Uncertain	0.86	D
MetaRNN	Benign	0.0016	T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	1.6	L
PhyloP100		4.1
PrimateAI	Uncertain	0.50	T
PROVEAN	Uncertain	-3.1	D
REVEL	Benign	0.11
Sift	Uncertain	0.0070	D
Sift4G	Uncertain	0.011	D
Polyphen		0.92	P
Vest4		0.12
MPC		0.48
ClinPred		0.025	T
GERP RS		5.2
Varity_R		0.15
gMVP		0.43
Mutation Taster		=99/1	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		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: rs6971091; hg19: chr7-128363287; COSMIC: COSV59373294; COSMIC: COSV59373294;