rs4806659

Variant names:

• chr19-55313218-G-A
• rs4806659
• NM_001282011.2:c.506-163C>T

Variant summary

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

The NM_001282011.2(TMEM150B):​c.506-163C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.411 in 151,854 control chromosomes in the GnomAD database, including 13,398 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 0.41 (13398 hom., cov: 32)
• Consequence: TMEM150B NM_001282011.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.93
• Publications: 7 publications found

Genes affected

TMEM150B (HGNC:34415): (transmembrane protein 150B) This gene encodes a protein that belongs to the DRAM (damage-regulated autophagy modulator) family of membrane-spanning proteins. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Aug 2013]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.467 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001282011.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TMEM150B	NM_001282011.2	MANE Select	c.506-163C>T		intron	N/A	NP_001268940.1	A6NC51
	TMEM150B	NM_001085488.3		c.506-163C>T		intron	N/A	NP_001078957.1	A6NC51
	TMEM150B	NR_104066.2		n.661-163C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TMEM150B	ENST00000326652.9	TSL:1 MANE Select	c.506-163C>T		intron	N/A	ENSP00000320757.4	A6NC51
	TMEM150B	ENST00000586609.5	TSL:1	n.*246-163C>T		intron	N/A	ENSP00000466957.1	K7ENI3
	TMEM150B	ENST00000592603.5	TSL:1	n.*246-163C>T		intron	N/A	ENSP00000468745.1	K7ENI3

Frequencies

GnomAD3 genomes AF: 0.412 AC: 62441 AN: 151736 Hom.: 13388 Cov.: 32

Gnomad AFR AF: 0.357

Gnomad AMI AF: 0.369

Gnomad AMR AF: 0.443

Gnomad ASJ AF: 0.523

Gnomad EAS AF: 0.0799

Gnomad SAS AF: 0.483

Gnomad FIN AF: 0.398

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.453

Gnomad OTH AF: 0.440

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

GnomAD4 genome AF: 0.411 AC: 62484 AN: 151854 Hom.: 13398 Cov.: 32 AF XY: 0.408 AC XY: 30306 AN XY: 74214

African (AFR) AF: 0.357 AC: 14799 AN: 41406

American (AMR) AF: 0.443 AC: 6766 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.523 AC: 1815 AN: 3470

East Asian (EAS) AF: 0.0797 AC: 409 AN: 5134

South Asian (SAS) AF: 0.483 AC: 2326 AN: 4816

European-Finnish (FIN) AF: 0.398 AC: 4196 AN: 10550

Middle Eastern (MID) AF: 0.476 AC: 139 AN: 292

European-Non Finnish (NFE) AF: 0.453 AC: 30781 AN: 67908

Other (OTH) AF: 0.435 AC: 918 AN: 2108

Alfa AF: 0.425 Hom.: 21582

Bravo AF: 0.409

Asia WGS AF: 0.296 AC: 1031 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.24
DANN	Benign	0.79
PhyloP100		-1.9
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: rs4806659; hg19: chr19-55824586; COSMIC: COSV58595258; COSMIC: COSV58595258;