chr12-6229471-C-T

Variant names:

• chr12-6229471-C-T
• rs740839
• NM_001769.4:c.176-3161C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001769.4(CD9):​c.176-3161C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.597 in 152,150 control chromosomes in the GnomAD database, including 28,236 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 0.60 (28236 hom., cov: 33)
• Consequence: CD9 NM_001769.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.91
• Publications: 5 publications found

Genes affected

CD9 (HGNC:1709): (CD9 molecule) This gene encodes a member of the transmembrane 4 superfamily, also known as the tetraspanin family. Tetraspanins are cell surface glycoproteins with four transmembrane domains that form multimeric complexes with other cell surface proteins. The encoded protein functions in many cellular processes including differentiation, adhesion, and signal transduction, and expression of this gene plays a critical role in the suppression of cancer cell motility and metastasis. [provided by RefSeq, Jan 2011]

ENSG00000305396 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.774 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CD9	NM_001769.4	c.176-3161C>T		intron_variant	Intron 2 of 7	ENST00000009180.10	NP_001760.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD9	ENST00000009180.10	c.176-3161C>T		intron_variant	Intron 2 of 7	1	NM_001769.4	ENSP00000009180.4

Frequencies

GnomAD3 genomes AF: 0.597 AC: 90745 AN: 152032 Hom.: 28193 Cov.: 33

Gnomad AFR AF: 0.781

Gnomad AMI AF: 0.525

Gnomad AMR AF: 0.500

Gnomad ASJ AF: 0.614

Gnomad EAS AF: 0.430

Gnomad SAS AF: 0.524

Gnomad FIN AF: 0.496

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.540

Gnomad OTH AF: 0.603

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

GnomAD4 genome AF: 0.597 AC: 90845 AN: 152150 Hom.: 28236 Cov.: 33 AF XY: 0.592 AC XY: 44036 AN XY: 74358

African (AFR) AF: 0.781 AC: 32430 AN: 41522

American (AMR) AF: 0.500 AC: 7641 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.614 AC: 2129 AN: 3470

East Asian (EAS) AF: 0.430 AC: 2228 AN: 5184

South Asian (SAS) AF: 0.523 AC: 2523 AN: 4820

European-Finnish (FIN) AF: 0.496 AC: 5243 AN: 10562

Middle Eastern (MID) AF: 0.602 AC: 177 AN: 294

European-Non Finnish (NFE) AF: 0.540 AC: 36715 AN: 67986

Other (OTH) AF: 0.605 AC: 1281 AN: 2116

Alfa AF: 0.564 Hom.: 40880

Bravo AF: 0.606

Asia WGS AF: 0.471 AC: 1641 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.086
DANN	Benign	0.61
PhyloP100		-2.9
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: rs740839; hg19: chr12-6338637;