11-836172-G-GCCCCCA

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP6_Very_Strong BS2

The NM_004357.5(CD151):c.84+36_84+41dup variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00982 in 151,598 control chromosomes in the GnomAD database, including 3 homozygotes. Variant has been reported in ClinVar as Likely benign (★★).

• Frequency:
  • Genomes: 𝑓 0.0098 (3 hom., cov: 34)
  • Exomes 𝑓: 0.0081 (77 hom.)
  • Failed GnomAD Quality Control
• Consequence: CD151 NM_004357.5 intron
• Clinical Significance: Benign/Likely benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.0680

Genes affected

CD151 (HGNC:1630): (CD151 molecule (Raph blood group)) 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. This encoded protein is a cell surface glycoprotein that is known to complex with integrins and other transmembrane 4 superfamily proteins. It is involved in cellular processes including cell adhesion and may regulate integrin trafficking and/or function. This protein enhances cell motility, invasion and metastasis of cancer cells. Multiple alternatively spliced transcript variants that encode the same protein have been described for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP6: Variant 11-836172-G-GCCCCCA is Benign according to our data. Variant chr11-836172-G-GCCCCCA is described in ClinVar as [Likely_benign]. Clinvar id is 1556161.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BS2: High Homozygotes in GnomAd at 3 BG gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CD151	NM_004357.5	c.84+36_84+41dup		intron_variant		ENST00000397420.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CD151	ENST00000397420.9	c.84+36_84+41dup		intron_variant		1	NM_004357.5	P3

Frequencies

GnomAD3 genomes AF: 0.00983 AC: 1489 AN: 151482 Hom.: 3 Cov.: 34

Gnomad AFR AF: 0.00245

Gnomad AMI AF: 0.0435

Gnomad AMR AF: 0.00539

Gnomad ASJ AF: 0.000866

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000623

Gnomad FIN AF: 0.0210

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0152

Gnomad OTH AF: 0.00434

GnomAD3 exomes AF: 0.00556 AC: 1350 AN: 242670 Hom.: 9 AF XY: 0.00521 AC XY: 686 AN XY: 131704

Gnomad AFR exome AF: 0.000973

Gnomad AMR exome AF: 0.00393

Gnomad ASJ exome AF: 0.000508

Gnomad EAS exome AF: 0.0000551

Gnomad SAS exome AF: 0.000300

Gnomad FIN exome AF: 0.0149

Gnomad NFE exome AF: 0.00771

Gnomad OTH exome AF: 0.00688

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00806 AC: 11248 AN: 1395380 Hom.: 77 Cov.: 25 AF XY: 0.00806 AC XY: 5616 AN XY: 696890

Gnomad4 AFR exome AF: 0.00182

Gnomad4 AMR exome AF: 0.00398

Gnomad4 ASJ exome AF: 0.000582

Gnomad4 EAS exome AF: 0.0000509

Gnomad4 SAS exome AF: 0.000495

Gnomad4 FIN exome AF: 0.0198

Gnomad4 NFE exome AF: 0.00901

Gnomad4 OTH exome AF: 0.00751

GnomAD4 genome AF: 0.00982 AC: 1489 AN: 151598 Hom.: 3 Cov.: 34 AF XY: 0.00961 AC XY: 712 AN XY: 74088

Gnomad4 AFR AF: 0.00244

Gnomad4 AMR AF: 0.00538

Gnomad4 ASJ AF: 0.000866

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000623

Gnomad4 FIN AF: 0.0210

Gnomad4 NFE AF: 0.0152

Gnomad4 OTH AF: 0.00430

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Likely benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 13, 2019	See Variant Classification Assertion Criteria. -
Benign, criteria provided, single submitter	clinical testing	Invitae	Jan 21, 2024	- -

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs34987505; hg19: chr11-836172;