chr19-55322296-A-G

Variant names:

• chr19-55322296-A-G
• rs11668344
• NM_001282011.2:c.-58+352T>C

Variant summary

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

The NM_001282011.2(TMEM150B):​c.-58+352T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.347 in 152,000 control chromosomes in the GnomAD database, including 9,525 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 (9525 hom., cov: 31)
• Consequence: TMEM150B NM_001282011.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.585
• Publications: 46 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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.441 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TMEM150B	NM_001282011.2	c.-58+352T>C		intron_variant	Intron 2 of 7	ENST00000326652.9	NP_001268940.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TMEM150B	ENST00000326652.9	c.-58+352T>C		intron_variant	Intron 2 of 7	1	NM_001282011.2	ENSP00000320757.4

Frequencies

GnomAD3 genomes AF: 0.347 AC: 52684 AN: 151882 Hom.: 9499 Cov.: 31

Gnomad AFR AF: 0.370

Gnomad AMI AF: 0.214

Gnomad AMR AF: 0.367

Gnomad ASJ AF: 0.379

Gnomad EAS AF: 0.0814

Gnomad SAS AF: 0.456

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.352

Gnomad OTH AF: 0.352

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

GnomAD4 genome AF: 0.347 AC: 52758 AN: 152000 Hom.: 9525 Cov.: 31 AF XY: 0.343 AC XY: 25455 AN XY: 74316

African (AFR) AF: 0.370 AC: 15351 AN: 41456

American (AMR) AF: 0.368 AC: 5617 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.379 AC: 1315 AN: 3468

East Asian (EAS) AF: 0.0810 AC: 418 AN: 5162

South Asian (SAS) AF: 0.457 AC: 2194 AN: 4806

European-Finnish (FIN) AF: 0.276 AC: 2923 AN: 10580

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.352 AC: 23919 AN: 67952

Other (OTH) AF: 0.349 AC: 738 AN: 2112

Alfa AF: 0.346 Hom.: 23492

Bravo AF: 0.353

Asia WGS AF: 0.288 AC: 1001 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.9
DANN	Benign	0.72
PhyloP100		0.58
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs11668344; hg19: chr19-55833664;