chr19-55322817-G-A

Position:

• chr19-55322817-G-A

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TMEM150B	NM_001282011.2	c.-153-74C>T		intron_variant		ENST00000326652.9	NP_001268940.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TMEM150B	ENST00000326652.9	c.-153-74C>T		intron_variant		1	NM_001282011.2	ENSP00000320757	P1

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

Gnomad4 AFR exome AF: 0.922

Gnomad4 AMR exome AF: 0.488

Gnomad4 ASJ exome AF: 0.602

Gnomad4 EAS exome AF: 0.183

Gnomad4 SAS exome AF: 0.604

Gnomad4 FIN exome AF: 0.467

Gnomad4 NFE exome AF: 0.547

Gnomad4 OTH exome AF: 0.553

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

Gnomad4 AFR AF: 0.891

Gnomad4 AMR AF: 0.542

Gnomad4 ASJ AF: 0.597

Gnomad4 EAS AF: 0.188

Gnomad4 SAS AF: 0.587

Gnomad4 FIN AF: 0.521

Gnomad4 NFE AF: 0.543

Gnomad4 OTH AF: 0.614

Alfa AF: 0.592 Hom.: 8040

Bravo AF: 0.639

Asia WGS AF: 0.491 AC: 1710 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.64
DANN	Benign	0.35

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

Publications

LitVar

Other links and lift over

dbSNP: rs8113016; hg19: chr19-55834185;