rs10488012

chr7-141318708-G-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_001195278.2(TMEM178B):c.496+106004G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.134 in 152,164 control chromosomes in the GnomAD database, including 1,710 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 0.13 (1710 hom., cov: 33)
• Consequence: TMEM178B NM_001195278.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.882

Genes affected

TMEM178B (HGNC:44112): (transmembrane protein 178B) Predicted to be integral component of membrane. Predicted to be active in membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.3).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.184 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TMEM178B	NM_001195278.2	c.496+106004G>T		intron_variant		ENST00000565468.6
TMEM178B	XM_011515705.3	c.496+106004G>T		intron_variant
TMEM178B	XM_017011636.2	c.496+106004G>T		intron_variant
TMEM178B	XR_001744505.2	n.743+106004G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TMEM178B	ENST00000565468.6	c.496+106004G>T		intron_variant		5	NM_001195278.2	P1

Frequencies

GnomAD3 genomes AF: 0.134 AC: 20358 AN: 152046 Hom.: 1710 Cov.: 33

Gnomad AFR AF: 0.0511

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.209

Gnomad EAS AF: 0.0212

Gnomad SAS AF: 0.0635

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.187

Gnomad OTH AF: 0.154

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

GnomAD4 genome AF: 0.134 AC: 20360 AN: 152164 Hom.: 1710 Cov.: 33 AF XY: 0.129 AC XY: 9626 AN XY: 74400

Gnomad4 AFR AF: 0.0511

Gnomad4 AMR AF: 0.137

Gnomad4 ASJ AF: 0.209

Gnomad4 EAS AF: 0.0211

Gnomad4 SAS AF: 0.0640

Gnomad4 FIN AF: 0.163

Gnomad4 NFE AF: 0.187

Gnomad4 OTH AF: 0.154

Alfa AF: 0.169 Hom.: 1246

Bravo AF: 0.129

Asia WGS AF: 0.0610 AC: 214 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.30
Cadd	Benign	18
Dann	Benign	0.69

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs10488012; hg19: chr7-141018508;