10-43115110-C-T

Variant summary

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

The NM_020975.6(RET):c.2136+374C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.785 in 152,172 control chromosomes in the GnomAD database, including 47,429 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 0.78 (47429 hom., cov: 33)
• Consequence: RET NM_020975.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.94

Genes affected

RET (HGNC:9967): (ret proto-oncogene) This gene encodes a transmembrane receptor and member of the tyrosine protein kinase family of proteins. Binding of ligands such as GDNF (glial cell-line derived neurotrophic factor) and other related proteins to the encoded receptor stimulates receptor dimerization and activation of downstream signaling pathways that play a role in cell differentiation, growth, migration and survival. The encoded receptor is important in development of the nervous system, and the development of organs and tissues derived from the neural crest. This proto-oncogene can undergo oncogenic activation through both cytogenetic rearrangement and activating point mutations. Mutations in this gene are associated with Hirschsprung disease and central hypoventilation syndrome and have been identified in patients with renal agenesis. [provided by RefSeq, Sep 2017]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.875 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RET	NM_020975.6	c.2136+374C>T		intron_variant		ENST00000355710.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RET	ENST00000355710.8	c.2136+374C>T		intron_variant		5	NM_020975.6	P4

Frequencies

GnomAD3 genomes AF: 0.785 AC: 119294 AN: 152054 Hom.: 47377 Cov.: 33

Gnomad AFR AF: 0.883

Gnomad AMI AF: 0.822

Gnomad AMR AF: 0.765

Gnomad ASJ AF: 0.715

Gnomad EAS AF: 0.495

Gnomad SAS AF: 0.620

Gnomad FIN AF: 0.782

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.767

Gnomad OTH AF: 0.759

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

GnomAD4 genome AF: 0.785 AC: 119408 AN: 152172 Hom.: 47429 Cov.: 33 AF XY: 0.782 AC XY: 58148 AN XY: 74390

Gnomad4 AFR AF: 0.883

Gnomad4 AMR AF: 0.766

Gnomad4 ASJ AF: 0.715

Gnomad4 EAS AF: 0.495

Gnomad4 SAS AF: 0.622

Gnomad4 FIN AF: 0.782

Gnomad4 NFE AF: 0.767

Gnomad4 OTH AF: 0.759

Alfa AF: 0.764 Hom.: 7640

Bravo AF: 0.792

Asia WGS AF: 0.592 AC: 2059 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.18
Dann	Benign	0.76

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: rs2742233; hg19: chr10-43610558;