11-836172-GCCCCCA-G

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP6_Moderate

The NM_004357.5(CD151):c.84+36_84+41del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000294 in 1,547,352 control chromosomes in the GnomAD database, including 2 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.00021 (0 hom., cov: 32)
  • Exomes 𝑓: 0.00030 (2 hom.)
• Consequence: CD151 NM_004357.5 intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.0790

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 Likely_benign. Variant got -2 ACMG points.

• BP6: Variant 11-836172-GCCCCCA-G is Benign according to our data. Variant chr11-836172-GCCCCCA-G is described in ClinVar as [Likely_benign]. Clinvar id is 1631297.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.000211 AC: 32 AN: 151550 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.000121

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000657

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000383

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000310

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.000330 AC: 80 AN: 242670 Hom.: 1 AF XY: 0.000296 AC XY: 39 AN XY: 131704

Gnomad AFR exome AF: 0.000389

Gnomad AMR exome AF: 0.000234

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.000165

Gnomad SAS exome AF: 0.000167

Gnomad FIN exome AF: 0.000628

Gnomad NFE exome AF: 0.000406

Gnomad OTH exome AF: 0.000168

GnomAD4 exome AF: 0.000303 AC: 423 AN: 1395686 Hom.: 2 AF XY: 0.000274 AC XY: 191 AN XY: 697056

Gnomad4 AFR exome AF: 0.000247

Gnomad4 AMR exome AF: 0.000225

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.000992

Gnomad4 SAS exome AF: 0.000141

Gnomad4 FIN exome AF: 0.000426

Gnomad4 NFE exome AF: 0.000299

Gnomad4 OTH exome AF: 0.000258

GnomAD4 genome AF: 0.000211 AC: 32 AN: 151666 Hom.: 0 Cov.: 32 AF XY: 0.000216 AC XY: 16 AN XY: 74114

Gnomad4 AFR AF: 0.000121

Gnomad4 AMR AF: 0.0000656

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.000383

Gnomad4 NFE AF: 0.000310

Gnomad4 OTH AF: 0.00

Bravo AF: 0.000208

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Invitae

Jan 09, 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;