rs11062578

Positions:

• chr12-3218001-G-A

Variant summary

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

The NM_006675.5(TSPAN9):​c.63+16745G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0684 in 152,244 control chromosomes in the GnomAD database, including 438 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 0.068 (438 hom., cov: 32)
• Consequence: TSPAN9 NM_006675.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.04

Genes affected

TSPAN9 (HGNC:21640): (tetraspanin 9) The protein encoded by this gene is a member of the transmembrane 4 superfamily, also known as the tetraspanin family. Most of these members are cell-surface proteins that are characterized by the presence of four hydrophobic domains. The proteins mediate signal transduction events that play a role in the regulation of cell development, activation, growth and motility. Alternatively spliced transcripts encoding the same protein have been identified. [provided by RefSeq, Nov 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0901 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TSPAN9	NM_006675.5	c.63+16745G>A		intron_variant		ENST00000011898.10	NP_006666.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TSPAN9	ENST00000011898.10	c.63+16745G>A		intron_variant		1	NM_006675.5	ENSP00000011898.5

Frequencies

GnomAD3 genomes AF: 0.0683 AC: 10397 AN: 152126 Hom.: 433 Cov.: 32

Gnomad AFR AF: 0.0269

Gnomad AMI AF: 0.0757

Gnomad AMR AF: 0.0525

Gnomad ASJ AF: 0.0857

Gnomad EAS AF: 0.0658

Gnomad SAS AF: 0.0583

Gnomad FIN AF: 0.0982

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0920

Gnomad OTH AF: 0.0782

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

GnomAD4 genome AF: 0.0684 AC: 10411 AN: 152244 Hom.: 438 Cov.: 32 AF XY: 0.0675 AC XY: 5023 AN XY: 74436

Gnomad4 AFR AF: 0.0269

Gnomad4 AMR AF: 0.0524

Gnomad4 ASJ AF: 0.0857

Gnomad4 EAS AF: 0.0654

Gnomad4 SAS AF: 0.0591

Gnomad4 FIN AF: 0.0982

Gnomad4 NFE AF: 0.0920

Gnomad4 OTH AF: 0.0845

Alfa AF: 0.0854 Hom.: 549

Bravo AF: 0.0636

Asia WGS AF: 0.0950 AC: 330 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.028
DANN	Benign	0.69

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: rs11062578; hg19: chr12-3327167;