14-104509313-A-G

Position:

• chr14-104509313-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000415614.6(TMEM179):​c.523-34588T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.788 in 152,100 control chromosomes in the GnomAD database, including 47,304 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 0.79 (47304 hom., cov: 31)
• Consequence: TMEM179 ENST00000415614.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.84

Genes affected

TMEM179 (HGNC:20137): (transmembrane protein 179) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.08).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.811 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.104509313A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TMEM179	ENST00000415614.6	c.523-34588T>C		intron_variant		4		ENSP00000397763.2

Frequencies

GnomAD3 genomes AF: 0.788 AC: 119804 AN: 151982 Hom.: 47261 Cov.: 31

Gnomad AFR AF: 0.783

Gnomad AMI AF: 0.866

Gnomad AMR AF: 0.823

Gnomad ASJ AF: 0.803

Gnomad EAS AF: 0.799

Gnomad SAS AF: 0.641

Gnomad FIN AF: 0.812

Gnomad MID AF: 0.685

Gnomad NFE AF: 0.788

Gnomad OTH AF: 0.783

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

GnomAD4 genome AF: 0.788 AC: 119904 AN: 152100 Hom.: 47304 Cov.: 31 AF XY: 0.787 AC XY: 58486 AN XY: 74360

Gnomad4 AFR AF: 0.783

Gnomad4 AMR AF: 0.823

Gnomad4 ASJ AF: 0.803

Gnomad4 EAS AF: 0.800

Gnomad4 SAS AF: 0.641

Gnomad4 FIN AF: 0.812

Gnomad4 NFE AF: 0.788

Gnomad4 OTH AF: 0.783

Alfa AF: 0.793 Hom.: 8772

Bravo AF: 0.792

Asia WGS AF: 0.739 AC: 2570 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.42
DANN	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4983565; hg19: chr14-104975650;