14-104558177-G-A

Variant names:

• chr14-104558177-G-A
• rs4247039
• ENST00000415614.6:c.522+36988C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000415614.6(TMEM179):​c.522+36988C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.207 in 152,204 control chromosomes in the GnomAD database, including 3,807 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 0.21 (3807 hom., cov: 33)
• Consequence: TMEM179 ENST00000415614.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.501
• Publications: 2 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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.581 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000415614.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TMEM179	ENST00000415614.6	TSL:4	c.522+36988C>T		intron	N/A	ENSP00000397763.2

Frequencies

GnomAD3 genomes AF: 0.207 AC: 31458 AN: 152084 Hom.: 3797 Cov.: 33

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.0647

Gnomad AMR AF: 0.262

Gnomad ASJ AF: 0.0917

Gnomad EAS AF: 0.599

Gnomad SAS AF: 0.282

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.166

Gnomad OTH AF: 0.196

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

GnomAD4 genome AF: 0.207 AC: 31497 AN: 152204 Hom.: 3807 Cov.: 33 AF XY: 0.210 AC XY: 15663 AN XY: 74418

African (AFR) AF: 0.224 AC: 9297 AN: 41548

American (AMR) AF: 0.262 AC: 4008 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0917 AC: 318 AN: 3468

East Asian (EAS) AF: 0.599 AC: 3094 AN: 5168

South Asian (SAS) AF: 0.281 AC: 1356 AN: 4824

European-Finnish (FIN) AF: 0.153 AC: 1624 AN: 10610

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.166 AC: 11295 AN: 67994

Other (OTH) AF: 0.202 AC: 426 AN: 2110

Alfa AF: 0.196 Hom.: 1532

Bravo AF: 0.221

Asia WGS AF: 0.426 AC: 1481 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.19
DANN	Benign	0.51
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs4247039; hg19: chr14-105024514;