rs4806661

Variant names:

• chr19-55313293-A-T
• rs4806661
• NM_001282011.2:c.506-238T>A

Variant summary

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

The NM_001282011.2(TMEM150B):​c.506-238T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.414 in 151,752 control chromosomes in the GnomAD database, including 13,767 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 (13767 hom., cov: 31)
• Consequence: TMEM150B NM_001282011.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.836
• Publications: 10 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.523 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.506-238T>A		intron	N/A	NP_001268940.1	A6NC51
	TMEM150B	NM_001085488.3		c.506-238T>A		intron	N/A	NP_001078957.1	A6NC51
	TMEM150B	NR_104066.2		n.661-238T>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TMEM150B	ENST00000326652.9	TSL:1 MANE Select	c.506-238T>A		intron	N/A	ENSP00000320757.4	A6NC51
	TMEM150B	ENST00000586609.5	TSL:1	n.*246-238T>A		intron	N/A	ENSP00000466957.1	K7ENI3
	TMEM150B	ENST00000592603.5	TSL:1	n.*246-238T>A		intron	N/A	ENSP00000468745.1	K7ENI3

Frequencies

GnomAD3 genomes AF: 0.414 AC: 62755 AN: 151634 Hom.: 13735 Cov.: 31

Gnomad AFR AF: 0.529

Gnomad AMI AF: 0.322

Gnomad AMR AF: 0.399

Gnomad ASJ AF: 0.426

Gnomad EAS AF: 0.0822

Gnomad SAS AF: 0.473

Gnomad FIN AF: 0.324

Gnomad MID AF: 0.328

Gnomad NFE AF: 0.383

Gnomad OTH AF: 0.402

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

GnomAD4 genome AF: 0.414 AC: 62838 AN: 151752 Hom.: 13767 Cov.: 31 AF XY: 0.409 AC XY: 30288 AN XY: 74132

African (AFR) AF: 0.529 AC: 21892 AN: 41358

American (AMR) AF: 0.400 AC: 6104 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.426 AC: 1478 AN: 3472

East Asian (EAS) AF: 0.0818 AC: 421 AN: 5144

South Asian (SAS) AF: 0.473 AC: 2273 AN: 4806

European-Finnish (FIN) AF: 0.324 AC: 3407 AN: 10512

Middle Eastern (MID) AF: 0.329 AC: 96 AN: 292

European-Non Finnish (NFE) AF: 0.383 AC: 26032 AN: 67892

Other (OTH) AF: 0.399 AC: 842 AN: 2108

Alfa AF: 0.387 Hom.: 1474

Bravo AF: 0.424

Asia WGS AF: 0.311 AC: 1085 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.46
DANN	Benign	0.61
PhyloP100		-0.84
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: rs4806661; hg19: chr19-55824661;