19-55321516-G-A

Variant names:

• chr19-55321516-G-A
• rs734518
• NM_001282011.2:c.-57-423C>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.-57-423C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.472 in 151,770 control chromosomes in the GnomAD database, including 17,463 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 0.47 (17463 hom., cov: 30)
• Consequence: TMEM150B NM_001282011.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.989
• 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=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.487 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.-57-423C>T		intron	N/A	NP_001268940.1
	TMEM150B	NM_001085488.3		c.-8-472C>T		intron	N/A	NP_001078957.1
	TMEM150B	NR_104066.2		n.167-423C>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.-57-423C>T		intron	N/A	ENSP00000320757.4
	TMEM150B	ENST00000586609.5	TSL:1	n.-57-423C>T		intron	N/A	ENSP00000466957.1
	TMEM150B	ENST00000592603.5	TSL:1	n.-8-472C>T		intron	N/A	ENSP00000468745.1

Frequencies

GnomAD3 genomes AF: 0.472 AC: 71542 AN: 151648 Hom.: 17440 Cov.: 30

Gnomad AFR AF: 0.486

Gnomad AMI AF: 0.415

Gnomad AMR AF: 0.464

Gnomad ASJ AF: 0.577

Gnomad EAS AF: 0.0818

Gnomad SAS AF: 0.491

Gnomad FIN AF: 0.450

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.492

Gnomad OTH AF: 0.488

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

GnomAD4 genome AF: 0.472 AC: 71606 AN: 151770 Hom.: 17463 Cov.: 30 AF XY: 0.467 AC XY: 34623 AN XY: 74134

African (AFR) AF: 0.486 AC: 20097 AN: 41372

American (AMR) AF: 0.464 AC: 7061 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.577 AC: 2000 AN: 3468

East Asian (EAS) AF: 0.0814 AC: 420 AN: 5158

South Asian (SAS) AF: 0.492 AC: 2360 AN: 4800

European-Finnish (FIN) AF: 0.450 AC: 4734 AN: 10520

Middle Eastern (MID) AF: 0.507 AC: 148 AN: 292

European-Non Finnish (NFE) AF: 0.492 AC: 33391 AN: 67924

Other (OTH) AF: 0.483 AC: 1017 AN: 2106

Alfa AF: 0.485 Hom.: 8693

Bravo AF: 0.473

Asia WGS AF: 0.323 AC: 1128 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.1
DANN	Benign	0.76
PhyloP100		0.99
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: rs734518; hg19: chr19-55832884;