rs3791731

Positions:

• chr2-26190499-C-A

Variant summary

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

The XM_011532567.4(GAREM2):​c.1683+3184C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.121 in 152,648 control chromosomes in the GnomAD database, including 2,560 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 0.12 (2557 hom., cov: 32)
  • Exomes 𝑓: 0.048 (3 hom.)
• Consequence: GAREM2 XM_011532567.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.00

Genes affected

GAREM2 (HGNC:27172): (GRB2 associated regulator of MAPK1 subtype 2)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.724 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GAREM2	XM_011532567.4	c.1683+3184C>A		intron_variant			XP_011530869.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.121 AC: 18369 AN: 152046 Hom.: 2559 Cov.: 32

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.0866

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.0893

Gnomad EAS AF: 0.745

Gnomad SAS AF: 0.0753

Gnomad FIN AF: 0.0605

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0596

Gnomad OTH AF: 0.125

GnomAD4 exome AF: 0.0475 AC: 23 AN: 484 Hom.: 3 AF XY: 0.0448 AC XY: 13 AN XY: 290

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.167

Gnomad4 ASJ exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0429

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.121 AC: 18376 AN: 152164 Hom.: 2557 Cov.: 32 AF XY: 0.126 AC XY: 9403 AN XY: 74388

Gnomad4 AFR AF: 0.118

Gnomad4 AMR AF: 0.257

Gnomad4 ASJ AF: 0.0893

Gnomad4 EAS AF: 0.744

Gnomad4 SAS AF: 0.0747

Gnomad4 FIN AF: 0.0605

Gnomad4 NFE AF: 0.0596

Gnomad4 OTH AF: 0.122

Alfa AF: 0.0759 Hom.: 1059

Bravo AF: 0.143

Asia WGS AF: 0.331 AC: 1150 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.089
DANN	Benign	0.53

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs3791731; hg19: chr2-26413368;