14-104513149-T-C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

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

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.990 AC: 6846 AN: 6916

American (AMR) AF: 0.981 AC: 20366 AN: 20768

Ashkenazi Jewish (ASJ) AF: 0.989 AC: 6243 AN: 6314

East Asian (EAS) AF: 1.00 AC: 8640 AN: 8640

South Asian (SAS) AF: 0.920 AC: 44536 AN: 48434

European-Finnish (FIN) AF: 0.979 AC: 9577 AN: 9780

Middle Eastern (MID) AF: 0.970 AC: 797 AN: 822

European-Non Finnish (NFE) AF: 0.954 AC: 117972 AN: 123646

Other (OTH) AF: 0.962 AC: 10702 AN: 11130

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

African (AFR) AF: 0.991 AC: 41222 AN: 41598

American (AMR) AF: 0.977 AC: 14959 AN: 15312

Ashkenazi Jewish (ASJ) AF: 0.990 AC: 3439 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5170 AN: 5174

South Asian (SAS) AF: 0.927 AC: 4473 AN: 4826

European-Finnish (FIN) AF: 0.981 AC: 10424 AN: 10624

Middle Eastern (MID) AF: 0.993 AC: 292 AN: 294

European-Non Finnish (NFE) AF: 0.955 AC: 64937 AN: 68028

Other (OTH) AF: 0.973 AC: 2054 AN: 2110

Alfa AF: 0.962 Hom.: 15858

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
PhyloP100		0.81

Splicing

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

Other links and lift over

dbSNP: rs4264325; hg19: chr14-104979486;