rs16882396

Variant names:

• chr7-141188521-C-G
• rs16882396
• NM_001195278.2:c.383-24070C>G

Your query was ambiguous. Multiple possible variants found:

• chr7-141188521-C-G
• chr7-141188521-C-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.383-24070C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0274 in 152,276 control chromosomes in the GnomAD database, including 94 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 0.027 (94 hom., cov: 32)
• Consequence: TMEM178B NM_001195278.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08
• Publications: 4 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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.1 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TMEM178B	NM_001195278.2	c.383-24070C>G		intron_variant	Intron 1 of 3	ENST00000565468.6	NP_001182207.1
TMEM178B	XM_011515705.3	c.383-24070C>G		intron_variant	Intron 1 of 3		XP_011514007.1
TMEM178B	XM_017011636.2	c.383-24070C>G		intron_variant	Intron 1 of 3		XP_016867125.1
TMEM178B	XR_001744505.2	n.630-24070C>G		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TMEM178B	ENST00000565468.6	c.383-24070C>G		intron_variant	Intron 1 of 3	5	NM_001195278.2	ENSP00000456594.1
TMEM178B	ENST00000563442.1	n.301-24070C>G		intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes AF: 0.0274 AC: 4176 AN: 152158 Hom.: 96 Cov.: 32

Gnomad AFR AF: 0.00560

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.0199

Gnomad ASJ AF: 0.0559

Gnomad EAS AF: 0.108

Gnomad SAS AF: 0.0645

Gnomad FIN AF: 0.0272

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0324

Gnomad OTH AF: 0.0315

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

GnomAD4 genome AF: 0.0274 AC: 4173 AN: 152276 Hom.: 94 Cov.: 32 AF XY: 0.0283 AC XY: 2111 AN XY: 74468

African (AFR) AF: 0.00561 AC: 233 AN: 41560

American (AMR) AF: 0.0199 AC: 304 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0559 AC: 194 AN: 3470

East Asian (EAS) AF: 0.108 AC: 557 AN: 5178

South Asian (SAS) AF: 0.0651 AC: 314 AN: 4820

European-Finnish (FIN) AF: 0.0272 AC: 289 AN: 10616

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0324 AC: 2201 AN: 68022

Other (OTH) AF: 0.0307 AC: 65 AN: 2116

Alfa AF: 0.0176 Hom.: 7

Bravo AF: 0.0246

Asia WGS AF: 0.0660 AC: 228 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.80
DANN	Benign	0.42
PhyloP100		-1.1
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: rs16882396; hg19: chr7-140888321;