chr18-32446429-T-C

Position:

• chr18-32446429-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001242409.2(GAREM1):​c.121+23879A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.147 in 152,104 control chromosomes in the GnomAD database, including 2,001 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 0.15 (2001 hom., cov: 33)
• Consequence: GAREM1 NM_001242409.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.30

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.383 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GAREM1	NM_001242409.2	c.121+23879A>G		intron_variant		ENST00000269209.7	NP_001229338.1
GAREM1	NM_022751.3	c.121+23879A>G		intron_variant			NP_073588.1
GAREM1	XM_017025919.2	c.121+23879A>G		intron_variant			XP_016881408.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GAREM1	ENST00000269209.7	c.121+23879A>G		intron_variant		1	NM_001242409.2	ENSP00000269209	P4
GAREM1	ENST00000399218.8	c.121+23879A>G		intron_variant		2		ENSP00000382165	A1

Frequencies

GnomAD3 genomes AF: 0.146 AC: 22258 AN: 151986 Hom.: 1980 Cov.: 33

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.0537

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.118

Gnomad EAS AF: 0.397

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.139

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.143

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

GnomAD4 genome AF: 0.147 AC: 22334 AN: 152104 Hom.: 2001 Cov.: 33 AF XY: 0.149 AC XY: 11076 AN XY: 74334

Gnomad4 AFR AF: 0.194

Gnomad4 AMR AF: 0.152

Gnomad4 ASJ AF: 0.118

Gnomad4 EAS AF: 0.397

Gnomad4 SAS AF: 0.147

Gnomad4 FIN AF: 0.139

Gnomad4 NFE AF: 0.102

Gnomad4 OTH AF: 0.152

Alfa AF: 0.105 Hom.: 921

Bravo AF: 0.153

Asia WGS AF: 0.284 AC: 986 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.033
DANN	Benign	0.48

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

Publications

LitVar

Other links and lift over

dbSNP: rs11662168; hg19: chr18-30026392;