14-104509313-A-G

Variant names:

• chr14-104509313-A-G
• rs4983565
• ENST00000415614.6:c.523-34588T>C

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]

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TMEM179	ENST00000415614.6	c.523-34588T>C		intron_variant	Intron 3 of 3	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;