chr16-29956113-A-G

Variant names:

• chr16-29956113-A-G
• rs4788196
• ENST00000414689.6:c.-34-6997A>G

Variant summary

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

The ENST00000414689.6(TMEM219):​c.-34-6997A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.432 in 152,092 control chromosomes in the GnomAD database, including 14,219 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 0.43 (14219 hom., cov: 33)
• Consequence: TMEM219 ENST00000414689.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.820
• Publications: 18 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=-1.03).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.465 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000414689.6. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TMEM219	ENST00000414689.6	TSL:1	c.-34-6997A>G		intron	N/A	ENSP00000388485.2	Q86XT9

Frequencies

GnomAD3 genomes AF: 0.432 AC: 65618 AN: 151974 Hom.: 14210 Cov.: 33

Gnomad AFR AF: 0.423

Gnomad AMI AF: 0.475

Gnomad AMR AF: 0.376

Gnomad ASJ AF: 0.442

Gnomad EAS AF: 0.408

Gnomad SAS AF: 0.482

Gnomad FIN AF: 0.422

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.450

Gnomad OTH AF: 0.395

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

GnomAD4 genome AF: 0.432 AC: 65656 AN: 152092 Hom.: 14219 Cov.: 33 AF XY: 0.431 AC XY: 32007 AN XY: 74332

African (AFR) AF: 0.423 AC: 17548 AN: 41482

American (AMR) AF: 0.376 AC: 5730 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.442 AC: 1534 AN: 3468

East Asian (EAS) AF: 0.408 AC: 2114 AN: 5176

South Asian (SAS) AF: 0.481 AC: 2322 AN: 4824

European-Finnish (FIN) AF: 0.422 AC: 4469 AN: 10582

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.450 AC: 30567 AN: 67988

Other (OTH) AF: 0.392 AC: 827 AN: 2110

Alfa AF: 0.678 Hom.: 7269

Bravo AF: 0.422

Asia WGS AF: 0.366 AC: 1278 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.50
PhyloP100		-0.82
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: rs4788196; hg19: chr16-29967434;