rs1861243

Positions:

• chr2-39729696-T-C

Variant summary

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

The XM_024452702.2(TMEM178A):​c.401-5533T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.62 in 152,058 control chromosomes in the GnomAD database, including 31,037 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 0.62 (31037 hom., cov: 32)
• Consequence: TMEM178A XM_024452702.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.579

Genes affected

TMEM178A (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.826 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TMEM178A	XM_024452702.2	c.401-5533T>C		intron_variant			XP_024308470.1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.619 AC: 94107 AN: 151940 Hom.: 30977 Cov.: 32

Gnomad AFR AF: 0.833

Gnomad AMI AF: 0.470

Gnomad AMR AF: 0.650

Gnomad ASJ AF: 0.477

Gnomad EAS AF: 0.837

Gnomad SAS AF: 0.580

Gnomad FIN AF: 0.533

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.492

Gnomad OTH AF: 0.602

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

GnomAD4 genome AF: 0.620 AC: 94220 AN: 152058 Hom.: 31037 Cov.: 32 AF XY: 0.622 AC XY: 46214 AN XY: 74322

Gnomad4 AFR AF: 0.833

Gnomad4 AMR AF: 0.651

Gnomad4 ASJ AF: 0.477

Gnomad4 EAS AF: 0.837

Gnomad4 SAS AF: 0.579

Gnomad4 FIN AF: 0.533

Gnomad4 NFE AF: 0.492

Gnomad4 OTH AF: 0.603

Alfa AF: 0.568 Hom.: 3242

Bravo AF: 0.642

Asia WGS AF: 0.710 AC: 2467 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.2
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1861243; hg19: chr2-39956836;