14-104513149-T-C

Position:

• chr14-104513149-T-C

Variant summary

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

The ENST00000415614.6(TMEM179):​c.523-38424A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.961 in 388,800 control chromosomes in the GnomAD database, including 179,608 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 0.97 (71785 hom., cov: 34)
  • Exomes 𝑓: 0.95 (107823 hom.)
• Consequence: TMEM179 ENST00000415614.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.809

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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.983 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TMEM179	ENST00000415614.6	c.523-38424A>G		intron_variant		4		ENSP00000397763

Frequencies

GnomAD3 genomes AF: 0.970 AC: 147741 AN: 152232 Hom.: 71724 Cov.: 34

Gnomad AFR AF: 0.991

Gnomad AMI AF: 0.977

Gnomad AMR AF: 0.977

Gnomad ASJ AF: 0.990

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.927

Gnomad FIN AF: 0.981

Gnomad MID AF: 0.994

Gnomad NFE AF: 0.955

Gnomad OTH AF: 0.973

GnomAD4 exome AF: 0.954 AC: 225679 AN: 236450 Hom.: 107823 AF XY: 0.950 AC XY: 124389 AN XY: 130890

Gnomad4 AFR exome AF: 0.990

Gnomad4 AMR exome AF: 0.981

Gnomad4 ASJ exome AF: 0.989

Gnomad4 EAS exome AF: 1.00

Gnomad4 SAS exome AF: 0.920

Gnomad4 FIN exome AF: 0.979

Gnomad4 NFE exome AF: 0.954

Gnomad4 OTH exome AF: 0.962

GnomAD4 genome AF: 0.971 AC: 147861 AN: 152350 Hom.: 71785 Cov.: 34 AF XY: 0.972 AC XY: 72385 AN XY: 74498

Gnomad4 AFR AF: 0.991

Gnomad4 AMR AF: 0.977

Gnomad4 ASJ AF: 0.990

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.927

Gnomad4 FIN AF: 0.981

Gnomad4 NFE AF: 0.955

Gnomad4 OTH AF: 0.973

Alfa AF: 0.964 Hom.: 12327

Bravo AF: 0.972

Asia WGS AF: 0.973 AC: 3384 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	7.1
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4264325; hg19: chr14-104979486;