rs933360

chr7-50690548-C-T

Variant summary

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

The NM_001350814.2(GRB10):c.139+13273G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.612 in 152,114 control chromosomes in the GnomAD database, including 31,266 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 0.61 (31266 hom., cov: 33)
• Consequence: GRB10 NM_001350814.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.875

Genes affected

GRB10 (HGNC:4564): (growth factor receptor bound protein 10) The product of this gene belongs to a small family of adapter proteins that are known to interact with a number of receptor tyrosine kinases and signaling molecules. This gene encodes a growth factor receptor-binding protein that interacts with insulin receptors and insulin-like growth-factor receptors. Overexpression of some isoforms of the encoded protein inhibits tyrosine kinase activity and results in growth suppression. This gene is imprinted in a highly isoform- and tissue-specific manner, with expression observed from the paternal allele in the brain, and from the maternal allele in the placental trophoblasts. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Oct 2010]

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 (NFE) allele frequency at 95% confidence interval = 0.739 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GRB10	NM_001350814.2	c.139+13273G>A		intron_variant		ENST00000401949.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GRB10	ENST00000401949.6	c.139+13273G>A		intron_variant		1	NM_001350814.2	P3

Frequencies

GnomAD3 genomes AF: 0.612 AC: 93008 AN: 151996 Hom.: 31269 Cov.: 33

Gnomad AFR AF: 0.316

Gnomad AMI AF: 0.776

Gnomad AMR AF: 0.716

Gnomad ASJ AF: 0.835

Gnomad EAS AF: 0.740

Gnomad SAS AF: 0.681

Gnomad FIN AF: 0.561

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.744

Gnomad OTH AF: 0.685

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

GnomAD4 genome AF: 0.612 AC: 93025 AN: 152114 Hom.: 31266 Cov.: 33 AF XY: 0.606 AC XY: 45071 AN XY: 74356

Gnomad4 AFR AF: 0.316

Gnomad4 AMR AF: 0.716

Gnomad4 ASJ AF: 0.835

Gnomad4 EAS AF: 0.739

Gnomad4 SAS AF: 0.680

Gnomad4 FIN AF: 0.561

Gnomad4 NFE AF: 0.744

Gnomad4 OTH AF: 0.687

Alfa AF: 0.734 Hom.: 84907

Bravo AF: 0.606

Asia WGS AF: 0.724 AC: 2519 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	0.15
Dann	Benign	0.60

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: rs933360; hg19: chr7-50758245;