rs739091

chr22-39921122-C-A

Variant summary

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

The NM_004810.4(GRAP2):c.-15+19792C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.332 in 152,010 control chromosomes in the GnomAD database, including 10,208 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 0.33 (10208 hom., cov: 31)
• Consequence: GRAP2 NM_004810.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23

Genes affected

GRAP2 (HGNC:4563): (GRB2 related adaptor protein 2) This gene encodes a member of the GRB2/Sem5/Drk family. This member is an adaptor-like protein involved in leukocyte-specific protein-tyrosine kinase signaling. Like its related family member, GRB2-related adaptor protein (GRAP), this protein contains an SH2 domain flanked by two SH3 domains. This protein interacts with other proteins, such as GRB2-associated binding protein 1 (GAB1) and the SLP-76 leukocyte protein (LCP2), through its SH3 domains. Multiple alternatively spliced transcript variants encoding distinct isoforms have been found for this gene. [provided by RefSeq, Apr 2014]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.435 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GRAP2	NM_004810.4	c.-15+19792C>A		intron_variant		ENST00000344138.9
GRAP2	XM_047441607.1	c.-14-25971C>A		intron_variant
GRAP2	XM_047441608.1	c.92+19792C>A		intron_variant
GRAP2	XR_007067995.1	n.247+19792C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GRAP2	ENST00000344138.9	c.-15+19792C>A		intron_variant		1	NM_004810.4	P1

Frequencies

GnomAD3 genomes AF: 0.332 AC: 50402 AN: 151892 Hom.: 10214 Cov.: 31

Gnomad AFR AF: 0.0891

Gnomad AMI AF: 0.465

Gnomad AMR AF: 0.430

Gnomad ASJ AF: 0.481

Gnomad EAS AF: 0.237

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.420

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.439

Gnomad OTH AF: 0.368

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

GnomAD4 genome AF: 0.332 AC: 50400 AN: 152010 Hom.: 10208 Cov.: 31 AF XY: 0.332 AC XY: 24708 AN XY: 74318

Gnomad4 AFR AF: 0.0890

Gnomad4 AMR AF: 0.431

Gnomad4 ASJ AF: 0.481

Gnomad4 EAS AF: 0.238

Gnomad4 SAS AF: 0.348

Gnomad4 FIN AF: 0.420

Gnomad4 NFE AF: 0.439

Gnomad4 OTH AF: 0.365

Alfa AF: 0.414 Hom.: 6422

Bravo AF: 0.326

Asia WGS AF: 0.269 AC: 936 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	0.34
Dann	Benign	0.51

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: rs739091; hg19: chr22-40317126;