chr4-82497357-G-A

Position:

• chr4-82497357-G-A

Variant summary

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

The NM_001080506.3(TMEM150C):​c.236-1162C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.907 in 152,278 control chromosomes in the GnomAD database, including 62,851 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 0.91 (62851 hom., cov: 32)
• Consequence: TMEM150C NM_001080506.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.209

Genes affected

TMEM150C (HGNC:37263): (transmembrane protein 150C) This gene encodes a transmembrane protein component of a mechanosensitve ion channel that is activated by mechanical stimuli in various cell types and confers slowly adapting, mechanically activated currents in dorsal root ganglion neurons. Mechanically activated ion channels are sensors that are critical for hearing, touch, pain, and blood pressure regulation. [provided by RefSeq, Jul 2017]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.52).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TMEM150C	NM_001080506.3	c.236-1162C>T		intron_variant		ENST00000449862.7
TMEM150C	NM_001353454.2	c.326-1162C>T		intron_variant
TMEM150C	NM_001353455.2	c.236-1162C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TMEM150C	ENST00000449862.7	c.236-1162C>T		intron_variant		1	NM_001080506.3	P1
TMEM150C	ENST00000508701.5	c.236-1162C>T		intron_variant		4
TMEM150C	ENST00000515780.6	c.236-1162C>T		intron_variant		2		P1

Frequencies

GnomAD3 genomes AF: 0.907 AC: 138011 AN: 152160 Hom.: 62785 Cov.: 32

Gnomad AFR AF: 0.970

Gnomad AMI AF: 0.964

Gnomad AMR AF: 0.913

Gnomad ASJ AF: 0.894

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.906

Gnomad FIN AF: 0.907

Gnomad MID AF: 0.873

Gnomad NFE AF: 0.860

Gnomad OTH AF: 0.907

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

GnomAD4 genome AF: 0.907 AC: 138136 AN: 152278 Hom.: 62851 Cov.: 32 AF XY: 0.911 AC XY: 67820 AN XY: 74450

Gnomad4 AFR AF: 0.970

Gnomad4 AMR AF: 0.913

Gnomad4 ASJ AF: 0.894

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.906

Gnomad4 FIN AF: 0.907

Gnomad4 NFE AF: 0.860

Gnomad4 OTH AF: 0.908

Alfa AF: 0.878 Hom.: 25324

Bravo AF: 0.910

Asia WGS AF: 0.962 AC: 3328 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	12
DANN	Benign	0.70

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: rs6840169; hg19: chr4-83418510;