14-104513149-T-C

Variant names:

• chr14-104513149-T-C
• rs4264325
• ENST00000415614.6:c.523-38424A>G

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TMEM179	ENST00000415614.6	c.523-38424A>G		intron_variant	Intron 3 of 3	4		ENSP00000397763.2

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;