rs11901

Variant names:

• chr16-29972749-C-G
• rs11901
• NM_001083613.2:c.*34-201C>G

Variant summary

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

The NM_001083613.2(TMEM219):​c.*34-201C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.378 in 152,072 control chromosomes in the GnomAD database, including 11,470 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 0.38 (11470 hom., cov: 32)
• Consequence: TMEM219 NM_001083613.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.111
• Publications: 11 publications found

Genes affected

TMEM219 (HGNC:25201): (transmembrane protein 219) Predicted to be involved in apoptotic process. Predicted to be located in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.472 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TMEM219	NM_001083613.2	c.*34-201C>G		intron_variant	Intron 5 of 5	ENST00000279396.11	NP_001077082.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TMEM219	ENST00000279396.11	c.*34-201C>G		intron_variant	Intron 5 of 5	1	NM_001083613.2	ENSP00000279396.6

Frequencies

GnomAD3 genomes AF: 0.378 AC: 57456 AN: 151954 Hom.: 11471 Cov.: 32

Gnomad AFR AF: 0.243

Gnomad AMI AF: 0.477

Gnomad AMR AF: 0.352

Gnomad ASJ AF: 0.439

Gnomad EAS AF: 0.399

Gnomad SAS AF: 0.489

Gnomad FIN AF: 0.406

Gnomad MID AF: 0.385

Gnomad NFE AF: 0.448

Gnomad OTH AF: 0.360

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

GnomAD4 genome AF: 0.378 AC: 57459 AN: 152072 Hom.: 11470 Cov.: 32 AF XY: 0.377 AC XY: 28046 AN XY: 74330

African (AFR) AF: 0.243 AC: 10083 AN: 41486

American (AMR) AF: 0.351 AC: 5369 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.439 AC: 1523 AN: 3470

East Asian (EAS) AF: 0.399 AC: 2068 AN: 5180

South Asian (SAS) AF: 0.489 AC: 2360 AN: 4828

European-Finnish (FIN) AF: 0.406 AC: 4284 AN: 10560

Middle Eastern (MID) AF: 0.384 AC: 112 AN: 292

European-Non Finnish (NFE) AF: 0.448 AC: 30474 AN: 67962

Other (OTH) AF: 0.358 AC: 754 AN: 2108

Alfa AF: 0.408 Hom.: 1646

Bravo AF: 0.362

Asia WGS AF: 0.355 AC: 1238 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	5.0
DANN	Benign	0.78
PhyloP100		-0.11
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: rs11901; hg19: chr16-29984070;