chr7-141284199-C-T

Variant names:

• chr7-141284199-C-T
• rs217007
• NM_001195278.2:c.496+71495C>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+71495C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 152,222 control chromosomes in the GnomAD database, including 1,332 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 (1332 hom., cov: 32)
• Consequence: TMEM178B NM_001195278.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.87
• Publications: 1 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.222 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TMEM178B	NM_001195278.2	c.496+71495C>T		intron_variant	Intron 2 of 3	ENST00000565468.6	NP_001182207.1
TMEM178B	XM_011515705.3	c.496+71495C>T		intron_variant	Intron 2 of 3		XP_011514007.1
TMEM178B	XM_017011636.2	c.496+71495C>T		intron_variant	Intron 2 of 3		XP_016867125.1
TMEM178B	XR_001744505.2	n.743+71495C>T		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TMEM178B	ENST00000565468.6	c.496+71495C>T		intron_variant	Intron 2 of 3	5	NM_001195278.2	ENSP00000456594.1

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16317 AN: 152104 Hom.: 1330 Cov.: 32

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.0713

Gnomad ASJ AF: 0.0331

Gnomad EAS AF: 0.00327

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.0246

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0684

Gnomad OTH AF: 0.0977

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

GnomAD4 genome AF: 0.107 AC: 16333 AN: 152222 Hom.: 1332 Cov.: 32 AF XY: 0.104 AC XY: 7707 AN XY: 74428

African (AFR) AF: 0.226 AC: 9374 AN: 41502

American (AMR) AF: 0.0711 AC: 1088 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0331 AC: 115 AN: 3470

East Asian (EAS) AF: 0.00328 AC: 17 AN: 5186

South Asian (SAS) AF: 0.122 AC: 587 AN: 4822

European-Finnish (FIN) AF: 0.0246 AC: 261 AN: 10620

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.0684 AC: 4651 AN: 68006

Other (OTH) AF: 0.0967 AC: 204 AN: 2110

Alfa AF: 0.0818 Hom.: 2202

Bravo AF: 0.116

Asia WGS AF: 0.0610 AC: 212 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.032
DANN	Benign	0.66
PhyloP100		-2.9
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: rs217007; hg19: chr7-140983999;