7-141246833-C-T

Variant names:

• chr7-141246833-C-T
• rs2191934
• NM_001195278.2:c.496+34129C>T

Variant summary

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

The NM_001195278.2(TMEM178B):​c.496+34129C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.479 in 151,922 control chromosomes in the GnomAD database, including 17,797 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 0.48 (17797 hom., cov: 32)
• Consequence: TMEM178B NM_001195278.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.66
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.776 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001195278.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TMEM178B	NM_001195278.2	MANE Select	c.496+34129C>T		intron	N/A	NP_001182207.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TMEM178B	ENST00000565468.6	TSL:5 MANE Select	c.496+34129C>T		intron	N/A	ENSP00000456594.1

Frequencies

GnomAD3 genomes AF: 0.479 AC: 72649 AN: 151804 Hom.: 17784 Cov.: 32

Gnomad AFR AF: 0.469

Gnomad AMI AF: 0.477

Gnomad AMR AF: 0.527

Gnomad ASJ AF: 0.531

Gnomad EAS AF: 0.796

Gnomad SAS AF: 0.644

Gnomad FIN AF: 0.463

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.436

Gnomad OTH AF: 0.494

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

GnomAD4 genome AF: 0.479 AC: 72697 AN: 151922 Hom.: 17797 Cov.: 32 AF XY: 0.486 AC XY: 36094 AN XY: 74240

African (AFR) AF: 0.469 AC: 19404 AN: 41384

American (AMR) AF: 0.527 AC: 8046 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.531 AC: 1842 AN: 3472

East Asian (EAS) AF: 0.796 AC: 4104 AN: 5156

South Asian (SAS) AF: 0.645 AC: 3101 AN: 4806

European-Finnish (FIN) AF: 0.463 AC: 4892 AN: 10558

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.436 AC: 29646 AN: 67956

Other (OTH) AF: 0.495 AC: 1045 AN: 2112

Alfa AF: 0.464 Hom.: 16233

Bravo AF: 0.480

Asia WGS AF: 0.691 AC: 2402 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.066
DANN	Benign	0.53
PhyloP100		-2.7
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2191934; hg19: chr7-140946633;