Variant chr7-141113257-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001195278.2(TMEM178B):c.382+38565C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.319 in 152,058 control chromosomes in the GnomAD database, including 9,723 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 0.32 ( 9723 hom., cov: 32)

Consequence

TMEM178B
NM_001195278.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.25

Variant links:

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]

TMEM178B links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.76).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.454 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE
TMEM178B	NM_001195278.2 linkuse as main transcript	c.382+38565C>T	intron_variant	ENST00000565468.6
TMEM178B	XM_011515705.3 linkuse as main transcript	c.382+38565C>T	intron_variant
TMEM178B	XM_017011636.2 linkuse as main transcript	c.382+38565C>T	intron_variant
TMEM178B	XR_001744505.2 linkuse as main transcript	n.629+38565C>T	intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TMEM178B	ENST00000565468.6 linkuse as main transcript	c.382+38565C>T		intron_variant		5	NM_001195278.2	P1
TMEM178B	ENST00000563442.1 linkuse as main transcript	n.300+38565C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes

AF:

0.319

AC:

48477

AN:

151940

Hom.:

9728

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0935

Gnomad AMI

AF:

0.335

Gnomad AMR

AF:

0.349

Gnomad ASJ

AF:

0.374

Gnomad EAS

AF:

0.160

Gnomad SAS

AF:

0.192

Gnomad FIN

AF:

0.374

Gnomad MID

AF:

0.287

Gnomad NFE

AF:

0.458

Gnomad OTH

AF:

0.354

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

GnomAD4 genome

AF:

0.319

AC:

48470

AN:

152058

Hom.:

9723

Cov.:

AF XY:

0.312

AC XY:

23193

AN XY:

74314

show subpopulations

Gnomad4 AFR

AF:

0.0933

Gnomad4 AMR

AF:

0.349

Gnomad4 ASJ

AF:

0.374

Gnomad4 EAS

AF:

0.160

Gnomad4 SAS

AF:

0.193

Gnomad4 FIN

AF:

0.374

Gnomad4 NFE

AF:

0.458

Gnomad4 OTH

AF:

0.353

Alfa

AF:

0.366

Hom.:

1966

Bravo

AF:

0.309

Asia WGS

AF:

0.184

AC:

643

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.76

CADD

Benign

9.4

DANN

Benign

0.76

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.040

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over