19-55322817-G-A

Variant names:

• chr19-55322817-G-A
• rs8113016
• NM_001282011.2:c.-153-74C>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.-153-74C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.569 in 749,320 control chromosomes in the GnomAD database, including 124,720 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 0.63 (32358 hom., cov: 30)
  • Exomes 𝑓: 0.55 (92362 hom.)
• Consequence: TMEM150B NM_001282011.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14
• Publications: 12 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.883 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TMEM150B	NM_001282011.2	MANE Select	c.-153-74C>T		intron	N/A	NP_001268940.1
	TMEM150B	NM_001085488.3		c.-104-74C>T		intron	N/A	NP_001078957.1
	TMEM150B	NR_104066.2		n.71-74C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TMEM150B	ENST00000326652.9	TSL:1 MANE Select	c.-153-74C>T		intron	N/A	ENSP00000320757.4
	TMEM150B	ENST00000586609.5	TSL:1	n.-153-74C>T		intron	N/A	ENSP00000466957.1
	TMEM150B	ENST00000592603.5	TSL:1	n.-104-74C>T		intron	N/A	ENSP00000468745.1

Frequencies

GnomAD3 genomes AF: 0.627 AC: 95175 AN: 151742 Hom.: 32288 Cov.: 30

Gnomad AFR AF: 0.891

Gnomad AMI AF: 0.453

Gnomad AMR AF: 0.542

Gnomad ASJ AF: 0.597

Gnomad EAS AF: 0.188

Gnomad SAS AF: 0.587

Gnomad FIN AF: 0.521

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.543

Gnomad OTH AF: 0.612

GnomAD4 exome AF: 0.554 AC: 330766 AN: 597460 Hom.: 92362 AF XY: 0.555 AC XY: 154894 AN XY: 279212

African (AFR) AF: 0.922 AC: 10170 AN: 11028

American (AMR) AF: 0.488 AC: 322 AN: 660

Ashkenazi Jewish (ASJ) AF: 0.602 AC: 2242 AN: 3724

East Asian (EAS) AF: 0.183 AC: 461 AN: 2526

South Asian (SAS) AF: 0.604 AC: 7111 AN: 11776

European-Finnish (FIN) AF: 0.467 AC: 100 AN: 214

Middle Eastern (MID) AF: 0.575 AC: 677 AN: 1178

European-Non Finnish (NFE) AF: 0.547 AC: 298974 AN: 547000

Other (OTH) AF: 0.553 AC: 10709 AN: 19354

GnomAD4 genome AF: 0.628 AC: 95308 AN: 151860 Hom.: 32358 Cov.: 30 AF XY: 0.621 AC XY: 46021 AN XY: 74136

African (AFR) AF: 0.891 AC: 36947 AN: 41464

American (AMR) AF: 0.542 AC: 8258 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.597 AC: 2071 AN: 3468

East Asian (EAS) AF: 0.188 AC: 957 AN: 5102

South Asian (SAS) AF: 0.587 AC: 2832 AN: 4826

European-Finnish (FIN) AF: 0.521 AC: 5480 AN: 10520

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.543 AC: 36876 AN: 67926

Other (OTH) AF: 0.614 AC: 1295 AN: 2108

Alfa AF: 0.584 Hom.: 12579

Bravo AF: 0.639

Asia WGS AF: 0.491 AC: 1710 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.64
DANN	Benign	0.35
PhyloP100		-1.1
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: rs8113016; hg19: chr19-55834185;