rs4806660

chr19-55313266-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001282011.2(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_001282011.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.178

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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.446 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TMEM150B	NM_001282011.2	c.506-211A>G		intron_variant		ENST00000326652.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TMEM150B	ENST00000326652.9	c.506-211A>G		intron_variant		1	NM_001282011.2	P1

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

Gnomad4 AFR AF: 0.365

Gnomad4 AMR AF: 0.374

Gnomad4 ASJ AF: 0.382

Gnomad4 EAS AF: 0.0798

Gnomad4 SAS AF: 0.462

Gnomad4 FIN AF: 0.305

Gnomad4 NFE AF: 0.363

Gnomad4 OTH AF: 0.350

Alfa AF: 0.356 Hom.: 3215

Bravo AF: 0.357

Asia WGS AF: 0.286 AC: 996 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	5.6
Dann	Benign	0.67

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

Publications

LitVar

Other links and lift over

dbSNP: rs4806660; hg19: chr19-55824634;