14-104517318-T-G

Variant names:

• chr14-104517318-T-G
• rs4983568
• ENST00000415614.6:c.523-42593A>C

Variant summary

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

The ENST00000415614.6(TMEM179):​c.523-42593A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.155 in 152,226 control chromosomes in the GnomAD database, including 2,828 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 0.15 (2828 hom., cov: 33)
• Consequence: TMEM179 ENST00000415614.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.91
• Publications: 1 publications found

Genes affected

TMEM179 (HGNC:20137): (transmembrane protein 179) Predicted to be integral component of 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.468 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000415614.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TMEM179	ENST00000415614.6	TSL:4	c.523-42593A>C		intron	N/A	ENSP00000397763.2

Frequencies

GnomAD3 genomes AF: 0.155 AC: 23535 AN: 152108 Hom.: 2815 Cov.: 33

Gnomad AFR AF: 0.0399

Gnomad AMI AF: 0.200

Gnomad AMR AF: 0.345

Gnomad ASJ AF: 0.130

Gnomad EAS AF: 0.482

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.120

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.163

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

GnomAD4 genome AF: 0.155 AC: 23560 AN: 152226 Hom.: 2828 Cov.: 33 AF XY: 0.161 AC XY: 11990 AN XY: 74426

African (AFR) AF: 0.0399 AC: 1657 AN: 41562

American (AMR) AF: 0.346 AC: 5291 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.130 AC: 452 AN: 3472

East Asian (EAS) AF: 0.483 AC: 2499 AN: 5170

South Asian (SAS) AF: 0.251 AC: 1211 AN: 4820

European-Finnish (FIN) AF: 0.120 AC: 1268 AN: 10602

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.156 AC: 10612 AN: 68010

Other (OTH) AF: 0.161 AC: 341 AN: 2114

Alfa AF: 0.151 Hom.: 555

Bravo AF: 0.169

Asia WGS AF: 0.347 AC: 1205 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.6
DANN	Benign	0.63
PhyloP100		-1.9

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs4983568; hg19: chr14-104983655;