rs17784515

chr11-44852959-G-Achr11-44852959-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_130783.5(TSPAN18):c.-152-7369G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.219 in 152,094 control chromosomes in the GnomAD database, including 4,882 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 0.22 (4882 hom., cov: 33)
• Consequence: TSPAN18 NM_130783.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.367

Genes affected

TSPAN18 (HGNC:20660): (tetraspanin 18) Predicted to be integral component of membrane. Predicted to be integral component of plasma 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 (NFE) allele frequency at 95% confidence interval = 0.326 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TSPAN18	NM_130783.5	c.-152-7369G>A		intron_variant		ENST00000520358.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TSPAN18	ENST00000520358.7	c.-152-7369G>A		intron_variant		5	NM_130783.5	P1

Frequencies

GnomAD3 genomes AF: 0.219 AC: 33358 AN: 151976 Hom.: 4887 Cov.: 33

Gnomad AFR AF: 0.0585

Gnomad AMI AF: 0.396

Gnomad AMR AF: 0.193

Gnomad ASJ AF: 0.238

Gnomad EAS AF: 0.0460

Gnomad SAS AF: 0.0737

Gnomad FIN AF: 0.305

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.330

Gnomad OTH AF: 0.234

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

GnomAD4 genome AF: 0.219 AC: 33334 AN: 152094 Hom.: 4882 Cov.: 33 AF XY: 0.215 AC XY: 16007 AN XY: 74322

Gnomad4 AFR AF: 0.0584

Gnomad4 AMR AF: 0.193

Gnomad4 ASJ AF: 0.238

Gnomad4 EAS AF: 0.0455

Gnomad4 SAS AF: 0.0730

Gnomad4 FIN AF: 0.305

Gnomad4 NFE AF: 0.330

Gnomad4 OTH AF: 0.232

Alfa AF: 0.296 Hom.: 9462

Bravo AF: 0.208

Asia WGS AF: 0.0530 AC: 186 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	0.097
Dann	Benign	0.78

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: rs17784515; hg19: chr11-44874510;