14-104517318-T-G

Position:

• chr14-104517318-T-G

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TMEM179	ENST00000415614.6	c.523-42593A>C		intron_variant		4

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

Gnomad4 AFR AF: 0.0399

Gnomad4 AMR AF: 0.346

Gnomad4 ASJ AF: 0.130

Gnomad4 EAS AF: 0.483

Gnomad4 SAS AF: 0.251

Gnomad4 FIN AF: 0.120

Gnomad4 NFE AF: 0.156

Gnomad4 OTH AF: 0.161

Alfa AF: 0.153 Hom.: 459

Bravo AF: 0.169

Asia WGS AF: 0.347 AC: 1205 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4983568; hg19: chr14-104983655;