rs902951

Variant names:

• chr18-32359314-T-A
• rs902951
• NM_001242409.2:c.262+33581A>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001242409.2(GAREM1):​c.262+33581A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 152,130 control chromosomes in the GnomAD database, including 1,425 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 0.10 (1425 hom., cov: 32)
• Consequence: GAREM1 NM_001242409.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.624
• Publications: 1 publications found

Genes affected

GAREM1 (HGNC:26136): (GRB2 associated regulator of MAPK1 subtype 1) This gene encodes an adaptor protein which functions in the epidermal growth factor (EGF) receptor-mediated signaling pathway. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2011]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.24 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001242409.2. 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
	GAREM1	NM_001242409.2	MANE Select	c.262+33581A>T		intron	N/A	NP_001229338.1	Q9H706-1
	GAREM1	NM_022751.3		c.262+33581A>T		intron	N/A	NP_073588.1	Q9H706-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GAREM1	ENST00000269209.7	TSL:1 MANE Select	c.262+33581A>T		intron	N/A	ENSP00000269209.6	Q9H706-1
	GAREM1	ENST00000399218.8	TSL:2	c.262+33581A>T		intron	N/A	ENSP00000382165.3	Q9H706-3
	GAREM1	ENST00000952372.1		c.262+33581A>T		intron	N/A	ENSP00000622431.1

Frequencies

GnomAD3 genomes AF: 0.102 AC: 15563 AN: 152012 Hom.: 1416 Cov.: 32

Gnomad AFR AF: 0.243

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.0583

Gnomad ASJ AF: 0.0239

Gnomad EAS AF: 0.00906

Gnomad SAS AF: 0.0624

Gnomad FIN AF: 0.0838

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0438

Gnomad OTH AF: 0.0832

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

GnomAD4 genome AF: 0.103 AC: 15619 AN: 152130 Hom.: 1425 Cov.: 32 AF XY: 0.103 AC XY: 7665 AN XY: 74388

African (AFR) AF: 0.244 AC: 10096 AN: 41448

American (AMR) AF: 0.0581 AC: 889 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0239 AC: 83 AN: 3472

East Asian (EAS) AF: 0.00889 AC: 46 AN: 5176

South Asian (SAS) AF: 0.0628 AC: 303 AN: 4822

European-Finnish (FIN) AF: 0.0838 AC: 887 AN: 10586

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0438 AC: 2981 AN: 68014

Other (OTH) AF: 0.0828 AC: 175 AN: 2114

Alfa AF: 0.0853 Hom.: 130

Bravo AF: 0.107

Asia WGS AF: 0.0460 AC: 160 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.14
DANN	Benign	0.58
PhyloP100		-0.62
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: rs902951; hg19: chr18-29939277;