chr19-55322092-C-T

Variant names:

• chr19-55322092-C-T
• rs11668309
• NM_001282011.2:c.-58+556G>A

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+556G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.306 in 152,064 control chromosomes in the GnomAD database, including 7,693 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 0.31 (7693 hom., cov: 31)
• Consequence: TMEM150B NM_001282011.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0720
• Publications: 14 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 = 0.439 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TMEM150B	NM_001282011.2	MANE Select	c.-58+556G>A		intron	N/A	NP_001268940.1	A6NC51
	TMEM150B	NM_001085488.3		c.-9+556G>A		intron	N/A	NP_001078957.1	A6NC51
	TMEM150B	NR_104066.2		n.166+556G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TMEM150B	ENST00000326652.9	TSL:1 MANE Select	c.-58+556G>A		intron	N/A	ENSP00000320757.4	A6NC51
	TMEM150B	ENST00000586609.5	TSL:1	n.-58+556G>A		intron	N/A	ENSP00000466957.1	K7ENI3
	TMEM150B	ENST00000592603.5	TSL:1	n.-9+556G>A		intron	N/A	ENSP00000468745.1	K7ENI3

Frequencies

GnomAD3 genomes AF: 0.306 AC: 46465 AN: 151946 Hom.: 7683 Cov.: 31

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.274

Gnomad AMR AF: 0.351

Gnomad ASJ AF: 0.378

Gnomad EAS AF: 0.0815

Gnomad SAS AF: 0.454

Gnomad FIN AF: 0.277

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.351

Gnomad OTH AF: 0.319

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

GnomAD4 genome AF: 0.306 AC: 46494 AN: 152064 Hom.: 7693 Cov.: 31 AF XY: 0.303 AC XY: 22538 AN XY: 74320

African (AFR) AF: 0.226 AC: 9376 AN: 41482

American (AMR) AF: 0.352 AC: 5365 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.378 AC: 1312 AN: 3468

East Asian (EAS) AF: 0.0811 AC: 419 AN: 5168

South Asian (SAS) AF: 0.455 AC: 2191 AN: 4814

European-Finnish (FIN) AF: 0.277 AC: 2925 AN: 10568

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.352 AC: 23901 AN: 67992

Other (OTH) AF: 0.316 AC: 668 AN: 2112

Alfa AF: 0.335 Hom.: 15850

Bravo AF: 0.306

Asia WGS AF: 0.278 AC: 967 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.6
DANN	Benign	0.73
PhyloP100		0.072
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.080		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: rs11668309; hg19: chr19-55833460;