rs11901

Positions:

• chr16-29972749-C-G

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
TMEM219	NM_001083613.2	c.*34-201C>G		intron_variant		ENST00000279396.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TMEM219	ENST00000279396.11	c.*34-201C>G		intron_variant		1	NM_001083613.2	P1

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

Gnomad4 AFR AF: 0.243

Gnomad4 AMR AF: 0.351

Gnomad4 ASJ AF: 0.439

Gnomad4 EAS AF: 0.399

Gnomad4 SAS AF: 0.489

Gnomad4 FIN AF: 0.406

Gnomad4 NFE AF: 0.448

Gnomad4 OTH AF: 0.358

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

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: rs11901; hg19: chr16-29984070;