rs217007

Positions:

• chr7-141284199-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+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

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=-0.96).
• 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/exons	MANE	UniProt
TMEM178B	NM_001195278.2	c.496+71495C>T		intron_variant		ENST00000565468.6
TMEM178B	XM_011515705.3	c.496+71495C>T		intron_variant
TMEM178B	XM_017011636.2	c.496+71495C>T		intron_variant
TMEM178B	XR_001744505.2	n.743+71495C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TMEM178B	ENST00000565468.6	c.496+71495C>T		intron_variant		5	NM_001195278.2	P1

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

Gnomad4 AFR AF: 0.226

Gnomad4 AMR AF: 0.0711

Gnomad4 ASJ AF: 0.0331

Gnomad4 EAS AF: 0.00328

Gnomad4 SAS AF: 0.122

Gnomad4 FIN AF: 0.0246

Gnomad4 NFE AF: 0.0684

Gnomad4 OTH AF: 0.0967

Alfa AF: 0.0718 Hom.: 980

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

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: rs217007; hg19: chr7-140983999;