rs6840169

Variant names:

• chr4-82497357-G-A
• rs6840169
• NM_001080506.3:c.236-1162C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001080506.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TMEM150C	NM_001080506.3	MANE Select	c.236-1162C>T		intron	N/A	NP_001073975.1
	TMEM150C	NM_001353454.2		c.326-1162C>T		intron	N/A	NP_001340383.1
	TMEM150C	NM_001353455.2		c.236-1162C>T		intron	N/A	NP_001340384.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TMEM150C	ENST00000449862.7	TSL:1 MANE Select	c.236-1162C>T		intron	N/A	ENSP00000403438.2
	TMEM150C	ENST00000515780.6	TSL:2	c.236-1162C>T		intron	N/A	ENSP00000420919.1
	TMEM150C	ENST00000508701.5	TSL:4	c.236-1162C>T		intron	N/A	ENSP00000421812.1

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

African (AFR) AF: 0.970 AC: 40347 AN: 41574

American (AMR) AF: 0.913 AC: 13964 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.894 AC: 3103 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5182 AN: 5184

South Asian (SAS) AF: 0.906 AC: 4376 AN: 4830

European-Finnish (FIN) AF: 0.907 AC: 9610 AN: 10598

Middle Eastern (MID) AF: 0.878 AC: 258 AN: 294

European-Non Finnish (NFE) AF: 0.860 AC: 58498 AN: 68010

Other (OTH) AF: 0.908 AC: 1919 AN: 2114

Alfa AF: 0.890 Hom.: 34239

Bravo AF: 0.910

Asia WGS AF: 0.962 AC: 3328 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	12
DANN	Benign	0.70
PhyloP100		0.21
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: rs6840169; hg19: chr4-83418510;