rs6943153

Variant names:

• chr7-50723882-T-C
• rs6943153
• NM_001350814.2:c.51+8390A>G

Your query was ambiguous. Multiple possible variants found:

• chr7-50723882-T-C
• chr7-50723882-T-G

Variant summary

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

The NM_001350814.2(GRB10):​c.51+8390A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.568 in 151,928 control chromosomes in the GnomAD database, including 26,893 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 0.57 (26893 hom., cov: 33)
• Consequence: GRB10 NM_001350814.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.62
• Publications: 45 publications found

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

Our verdict: Benign. The variant received -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 = 0.726 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GRB10	NM_001350814.2	c.51+8390A>G		intron_variant	Intron 4 of 18	ENST00000401949.6	NP_001337743.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GRB10	ENST00000401949.6	c.51+8390A>G		intron_variant	Intron 4 of 18	1	NM_001350814.2	ENSP00000385770.1

Frequencies

GnomAD3 genomes AF: 0.568 AC: 86274 AN: 151810 Hom.: 26897 Cov.: 33

Gnomad AFR AF: 0.312

Gnomad AMI AF: 0.734

Gnomad AMR AF: 0.582

Gnomad ASJ AF: 0.768

Gnomad EAS AF: 0.746

Gnomad SAS AF: 0.680

Gnomad FIN AF: 0.499

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.694

Gnomad OTH AF: 0.637

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

GnomAD4 genome AF: 0.568 AC: 86278 AN: 151928 Hom.: 26893 Cov.: 33 AF XY: 0.561 AC XY: 41647 AN XY: 74254

African (AFR) AF: 0.312 AC: 12905 AN: 41348

American (AMR) AF: 0.581 AC: 8883 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.768 AC: 2667 AN: 3472

East Asian (EAS) AF: 0.745 AC: 3844 AN: 5158

South Asian (SAS) AF: 0.679 AC: 3273 AN: 4822

European-Finnish (FIN) AF: 0.499 AC: 5261 AN: 10536

Middle Eastern (MID) AF: 0.803 AC: 236 AN: 294

European-Non Finnish (NFE) AF: 0.694 AC: 47187 AN: 67982

Other (OTH) AF: 0.640 AC: 1353 AN: 2114

Alfa AF: 0.663 Hom.: 106108

Bravo AF: 0.558

Asia WGS AF: 0.716 AC: 2491 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	2.1
DANN	Benign	0.65
PhyloP100		-1.6
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: rs6943153; hg19: chr7-50791579;