rs2716734

chr2-39720581-C-T

Variant summary

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

The XM_024452702.2(TMEM178A):c.401-14648C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.114 in 152,182 control chromosomes in the GnomAD database, including 2,234 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 0.11 (2234 hom., cov: 32)
• Consequence: TMEM178A XM_024452702.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28

Genes affected

TMEM178A (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.316 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TMEM178A	XM_024452702.2	c.401-14648C>T		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.113 AC: 17229 AN: 152064 Hom.: 2213 Cov.: 32

Gnomad AFR AF: 0.320

Gnomad AMI AF: 0.0527

Gnomad AMR AF: 0.0520

Gnomad ASJ AF: 0.0337

Gnomad EAS AF: 0.00597

Gnomad SAS AF: 0.0398

Gnomad FIN AF: 0.0187

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0352

Gnomad OTH AF: 0.0909

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

GnomAD4 genome AF: 0.114 AC: 17290 AN: 152182 Hom.: 2234 Cov.: 32 AF XY: 0.110 AC XY: 8171 AN XY: 74400

Gnomad4 AFR AF: 0.321

Gnomad4 AMR AF: 0.0519

Gnomad4 ASJ AF: 0.0337

Gnomad4 EAS AF: 0.00579

Gnomad4 SAS AF: 0.0398

Gnomad4 FIN AF: 0.0187

Gnomad4 NFE AF: 0.0352

Gnomad4 OTH AF: 0.0900

Alfa AF: 0.0401 Hom.: 411

Bravo AF: 0.126

Asia WGS AF: 0.0480 AC: 169 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.3
Dann	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2716734; hg19: chr2-39947721;