chr12-3218001-G-A

Variant names:

• chr12-3218001-G-A
• rs11062578
• NM_006675.5:c.63+16745G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006675.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TSPAN9	NM_006675.5	MANE Select	c.63+16745G>A		intron	N/A	NP_006666.1
	TSPAN9	NM_001168320.2		c.63+16745G>A		intron	N/A	NP_001161792.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TSPAN9	ENST00000011898.10	TSL:1 MANE Select	c.63+16745G>A		intron	N/A	ENSP00000011898.5
	TSPAN9	ENST00000407263.2	TSL:5	c.63+16745G>A		intron	N/A	ENSP00000384488.1
	TSPAN9	ENST00000537971.5	TSL:3	c.63+16745G>A		intron	N/A	ENSP00000444799.1

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

African (AFR) AF: 0.0269 AC: 1117 AN: 41558

American (AMR) AF: 0.0524 AC: 802 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0857 AC: 297 AN: 3464

East Asian (EAS) AF: 0.0654 AC: 339 AN: 5182

South Asian (SAS) AF: 0.0591 AC: 285 AN: 4820

European-Finnish (FIN) AF: 0.0982 AC: 1042 AN: 10610

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0920 AC: 6257 AN: 67992

Other (OTH) AF: 0.0845 AC: 178 AN: 2106

Alfa AF: 0.0819 Hom.: 777

Bravo AF: 0.0636

Asia WGS AF: 0.0950 AC: 330 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.028
DANN	Benign	0.69
PhyloP100		-3.0
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: rs11062578; hg19: chr12-3327167;