rs2540226

chr2-39731920-A-Cchr2-39731920-A-G

Variant summary

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

The XM_024452702.2(TMEM178A):c.401-3309A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.566 in 151,956 control chromosomes in the GnomAD database, including 25,056 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 0.57 (25056 hom., cov: 31)
• Consequence: TMEM178A XM_024452702.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.528

Genes affected

TMEM178A (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.749 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TMEM178A	XM_024452702.2	c.401-3309A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.566 AC: 85929 AN: 151838 Hom.: 25017 Cov.: 31

Gnomad AFR AF: 0.672

Gnomad AMI AF: 0.469

Gnomad AMR AF: 0.610

Gnomad ASJ AF: 0.463

Gnomad EAS AF: 0.770

Gnomad SAS AF: 0.566

Gnomad FIN AF: 0.532

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.489

Gnomad OTH AF: 0.552

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

GnomAD4 genome AF: 0.566 AC: 86016 AN: 151956 Hom.: 25056 Cov.: 31 AF XY: 0.569 AC XY: 42243 AN XY: 74268

Gnomad4 AFR AF: 0.672

Gnomad4 AMR AF: 0.611

Gnomad4 ASJ AF: 0.463

Gnomad4 EAS AF: 0.769

Gnomad4 SAS AF: 0.565

Gnomad4 FIN AF: 0.532

Gnomad4 NFE AF: 0.489

Gnomad4 OTH AF: 0.553

Alfa AF: 0.507 Hom.: 24419

Bravo AF: 0.579

Asia WGS AF: 0.667 AC: 2319 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.86
Dann	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2540226; hg19: chr2-39959060;