17-78139331-G-T

Variant names:

• chr17-78139331-G-T
• rs17773854
• NM_152468.5:c.1902+91G>T

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_152468.5(TMC8):​c.1902+91G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.449 in 1,459,682 control chromosomes in the GnomAD database, including 150,156 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.43 (14788 hom., cov: 32)
  • Exomes 𝑓: 0.45 (135368 hom.)
• Consequence: TMC8 NM_152468.5 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:3
• Conservation: PhyloP100: 2.47

Genes affected

TMC8 (HGNC:20474): (transmembrane channel like 8) Epidermodysplasia verruciformis (EV) is an autosomal recessive dermatosis characterized by abnormal susceptibility to human papillomaviruses (HPVs) and a high rate of progression to squamous cell carcinoma on sun-exposed skin. EV is caused by mutations in either of two adjacent genes located on chromosome 17q25.3. Both of these genes encode integral membrane proteins that localize to the endoplasmic reticulum and are predicted to form transmembrane channels. This gene encodes a transmembrane channel-like protein with 8 predicted transmembrane domains and 3 leucine zipper motifs. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BP6: Variant 17-78139331-G-T is Benign according to our data. Variant chr17-78139331-G-T is described in ClinVar as [Benign]. Clinvar id is 1250684.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.469 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TMC8	NM_152468.5	c.1902+91G>T		intron_variant	Intron 15 of 15	ENST00000318430.10	NP_689681.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TMC8	ENST00000318430.10	c.1902+91G>T		intron_variant	Intron 15 of 15	1	NM_152468.5	ENSP00000325561.4

Frequencies

GnomAD3 genomes AF: 0.434 AC: 65946 AN: 151874 Hom.: 14782 Cov.: 32

Gnomad AFR AF: 0.398

Gnomad AMI AF: 0.575

Gnomad AMR AF: 0.363

Gnomad ASJ AF: 0.548

Gnomad EAS AF: 0.231

Gnomad SAS AF: 0.394

Gnomad FIN AF: 0.485

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.474

Gnomad OTH AF: 0.455

GnomAD4 exome AF: 0.451 AC: 589602 AN: 1307690 Hom.: 135368 AF XY: 0.452 AC XY: 295358 AN XY: 653892

Gnomad4 AFR exome AF: 0.400

Gnomad4 AMR exome AF: 0.276

Gnomad4 ASJ exome AF: 0.552

Gnomad4 EAS exome AF: 0.228

Gnomad4 SAS exome AF: 0.405

Gnomad4 FIN exome AF: 0.478

Gnomad4 NFE exome AF: 0.468

Gnomad4 OTH exome AF: 0.453

GnomAD4 genome AF: 0.434 AC: 65990 AN: 151992 Hom.: 14788 Cov.: 32 AF XY: 0.430 AC XY: 31964 AN XY: 74300

Gnomad4 AFR AF: 0.398

Gnomad4 AMR AF: 0.363

Gnomad4 ASJ AF: 0.548

Gnomad4 EAS AF: 0.231

Gnomad4 SAS AF: 0.394

Gnomad4 FIN AF: 0.485

Gnomad4 NFE AF: 0.474

Gnomad4 OTH AF: 0.457

Alfa AF: 0.472 Hom.: 22718

Bravo AF: 0.425

Asia WGS AF: 0.331 AC: 1153 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Jul 09, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

-

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

not specified Benign:1

Jan 24, 2024

Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is classified as Benign based on local population frequency. This variant was detected in 50% of patients studied by a panel of primary immunodeficiencies. Number of patients: 44. Only high quality variants are reported. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	9.4
DANN	Benign	0.58

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.11		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: rs17773854; hg19: chr17-76135412;