rs4294750

Variant names:

• chr14-104496776-C-T
• rs4294750
• ENST00000415614.6:c.523-22051G>A

Variant summary

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

The ENST00000415614.6(TMEM179):​c.523-22051G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.456 in 152,082 control chromosomes in the GnomAD database, including 18,823 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 0.46 (18823 hom., cov: 32)
• Consequence: TMEM179 ENST00000415614.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.493
• Publications: 5 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=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.616 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.523-22051G>A		intron_variant	Intron 3 of 3	4		ENSP00000397763.2

Frequencies

GnomAD3 genomes AF: 0.456 AC: 69312 AN: 151962 Hom.: 18825 Cov.: 32

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.671

Gnomad AMR AF: 0.396

Gnomad ASJ AF: 0.607

Gnomad EAS AF: 0.237

Gnomad SAS AF: 0.377

Gnomad FIN AF: 0.653

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.621

Gnomad OTH AF: 0.488

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

GnomAD4 genome AF: 0.456 AC: 69305 AN: 152082 Hom.: 18823 Cov.: 32 AF XY: 0.455 AC XY: 33810 AN XY: 74352

African (AFR) AF: 0.174 AC: 7222 AN: 41482

American (AMR) AF: 0.395 AC: 6031 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.607 AC: 2108 AN: 3470

East Asian (EAS) AF: 0.236 AC: 1222 AN: 5180

South Asian (SAS) AF: 0.378 AC: 1820 AN: 4820

European-Finnish (FIN) AF: 0.653 AC: 6899 AN: 10568

Middle Eastern (MID) AF: 0.534 AC: 157 AN: 294

European-Non Finnish (NFE) AF: 0.621 AC: 42208 AN: 67970

Other (OTH) AF: 0.487 AC: 1026 AN: 2108

Alfa AF: 0.561 Hom.: 6648

Bravo AF: 0.424

Asia WGS AF: 0.303 AC: 1054 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	4.5
DANN	Benign	0.70
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs4294750; hg19: chr14-104963113;