7-141246833-C-T

Position:

• chr7-141246833-C-T

Variant summary

Our verdict is Benign. Variant got -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

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 -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TMEM178B	NM_001195278.2	c.496+34129C>T		intron_variant		ENST00000565468.6	NP_001182207.1
TMEM178B	XM_011515705.3	c.496+34129C>T		intron_variant			XP_011514007.1
TMEM178B	XM_017011636.2	c.496+34129C>T		intron_variant			XP_016867125.1
TMEM178B	XR_001744505.2	n.743+34129C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TMEM178B	ENST00000565468.6	c.496+34129C>T		intron_variant		5	NM_001195278.2	ENSP00000456594	P1

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

Gnomad4 AFR AF: 0.469

Gnomad4 AMR AF: 0.527

Gnomad4 ASJ AF: 0.531

Gnomad4 EAS AF: 0.796

Gnomad4 SAS AF: 0.645

Gnomad4 FIN AF: 0.463

Gnomad4 NFE AF: 0.436

Gnomad4 OTH AF: 0.495

Alfa AF: 0.460 Hom.: 10976

Bravo AF: 0.480

Asia WGS AF: 0.691 AC: 2402 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.066
DANN	Benign	0.53

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: rs2191934; hg19: chr7-140946633;