rs4806660

Variant names:

• chr19-55313266-T-C
• rs4806660
• NM_001282011.2:c.506-211A>G

Variant summary

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

The NM_001085488.3(TMEM150B):​c.506-211A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.354 in 151,994 control chromosomes in the GnomAD database, including 9,926 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 0.35 (9926 hom., cov: 31)
• Consequence: TMEM150B NM_001085488.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.178
• Publications: 19 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 = 0.446 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001085488.3. 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.506-211A>G		intron	N/A	NP_001268940.1
	TMEM150B	NM_001085488.3		c.506-211A>G		intron	N/A	NP_001078957.1
	TMEM150B	NR_104066.2		n.661-211A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TMEM150B	ENST00000326652.9	TSL:1 MANE Select	c.506-211A>G		intron	N/A	ENSP00000320757.4
	TMEM150B	ENST00000586609.5	TSL:1	n.*246-211A>G		intron	N/A	ENSP00000466957.1
	TMEM150B	ENST00000592603.5	TSL:1	n.*246-211A>G		intron	N/A	ENSP00000468745.1

Frequencies

GnomAD3 genomes AF: 0.354 AC: 53755 AN: 151876 Hom.: 9914 Cov.: 31

Gnomad AFR AF: 0.365

Gnomad AMI AF: 0.277

Gnomad AMR AF: 0.374

Gnomad ASJ AF: 0.382

Gnomad EAS AF: 0.0800

Gnomad SAS AF: 0.462

Gnomad FIN AF: 0.305

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.363

Gnomad OTH AF: 0.353

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

GnomAD4 genome AF: 0.354 AC: 53802 AN: 151994 Hom.: 9926 Cov.: 31 AF XY: 0.349 AC XY: 25922 AN XY: 74298

African (AFR) AF: 0.365 AC: 15129 AN: 41456

American (AMR) AF: 0.374 AC: 5715 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.382 AC: 1326 AN: 3470

East Asian (EAS) AF: 0.0798 AC: 412 AN: 5166

South Asian (SAS) AF: 0.462 AC: 2229 AN: 4822

European-Finnish (FIN) AF: 0.305 AC: 3221 AN: 10570

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.363 AC: 24690 AN: 67930

Other (OTH) AF: 0.350 AC: 738 AN: 2108

Alfa AF: 0.359 Hom.: 6196

Bravo AF: 0.357

Asia WGS AF: 0.286 AC: 996 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	5.6
DANN	Benign	0.67
PhyloP100		-0.18
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs4806660; hg19: chr19-55824634;