rs3181301

Positions:

• chr12-6236618-C-A
• chr12-6236618-C-T

Variant summary

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

The NM_001769.4(CD9):​c.621+343C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.49 in 420,900 control chromosomes in the GnomAD database, including 51,294 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 0.46 (16683 hom., cov: 33)
  • Exomes 𝑓: 0.50 (34611 hom.)
• Consequence: CD9 NM_001769.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0290

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]

LOC105369625 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.508 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CD9	NM_001769.4	c.621+343C>A		intron_variant		ENST00000009180.10	NP_001760.1
LOC105369625	XR_001748978.2	n.411+11605G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CD9	ENST00000009180.10	c.621+343C>A		intron_variant		1	NM_001769.4	ENSP00000009180	P1

Frequencies

GnomAD3 genomes AF: 0.464 AC: 70598 AN: 151996 Hom.: 16669 Cov.: 33

Gnomad AFR AF: 0.374

Gnomad AMI AF: 0.522

Gnomad AMR AF: 0.451

Gnomad ASJ AF: 0.596

Gnomad EAS AF: 0.421

Gnomad SAS AF: 0.469

Gnomad FIN AF: 0.490

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.512

Gnomad OTH AF: 0.494

GnomAD4 exome AF: 0.504 AC: 135447 AN: 268784 Hom.: 34611 Cov.: 0 AF XY: 0.504 AC XY: 69111 AN XY: 137056

Gnomad4 AFR exome AF: 0.376

Gnomad4 AMR exome AF: 0.438

Gnomad4 ASJ exome AF: 0.597

Gnomad4 EAS exome AF: 0.443

Gnomad4 SAS exome AF: 0.472

Gnomad4 FIN exome AF: 0.494

Gnomad4 NFE exome AF: 0.518

Gnomad4 OTH exome AF: 0.509

GnomAD4 genome AF: 0.464 AC: 70642 AN: 152116 Hom.: 16683 Cov.: 33 AF XY: 0.463 AC XY: 34430 AN XY: 74354

Gnomad4 AFR AF: 0.374

Gnomad4 AMR AF: 0.451

Gnomad4 ASJ AF: 0.596

Gnomad4 EAS AF: 0.422

Gnomad4 SAS AF: 0.469

Gnomad4 FIN AF: 0.490

Gnomad4 NFE AF: 0.512

Gnomad4 OTH AF: 0.497

Alfa AF: 0.480 Hom.: 8266

Bravo AF: 0.461

Asia WGS AF: 0.413 AC: 1437 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.78
DANN	Benign	0.55

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: rs3181301; hg19: chr12-6345784;