rs150709104

Variant names:

• chr11-837436-A-C
• rs150709104
• NM_004357.5:c.457-24A>C

Your query was ambiguous. Multiple possible variants found:

• chr11-837436-A-C
• chr11-837436-A-G

Variant summary

Our verdict is Benign. The variant received -16 ACMG points: 0P and 16B. BP4_Strong BP6_Very_Strong BS2

The NM_004357.5(CD151):​c.457-24A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00102 in 1,612,084 control chromosomes in the GnomAD database, including 8 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.0034 (2 hom., cov: 34)
  • Exomes 𝑓: 0.00077 (6 hom.)
• Consequence: CD151 NM_004357.5 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 1.86
• Publications: 1 publications found

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]

POLR2L (HGNC:9199): (RNA polymerase II, I and III subunit L) This gene encodes a subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. The product of this gene contains four conserved cysteines characteristic of an atypical zinc-binding domain. Like its counterpart in yeast, this subunit may be shared by the other two DNA-directed RNA polymerases. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -16 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BP6: Variant 11-837436-A-C is Benign according to our data. Variant chr11-837436-A-C is described in ClinVar as Benign. ClinVar VariationId is 1268369.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BS2: High Homozygotes in GnomAd4 at 2 AR,Unknown gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004357.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD151	NM_004357.5	MANE Select	c.457-24A>C		intron	N/A	NP_004348.2
	CD151	NM_001039490.2		c.457-24A>C		intron	N/A	NP_001034579.1	P48509
	CD151	NM_139029.2		c.457-24A>C		intron	N/A	NP_620598.1	P48509

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD151	ENST00000397420.9	TSL:1 MANE Select	c.457-24A>C		intron	N/A	ENSP00000380565.3	P48509
	CD151	ENST00000322008.9	TSL:1	c.457-24A>C		intron	N/A	ENSP00000324101.4	P48509
	CD151	ENST00000397421.5	TSL:1	c.457-24A>C		intron	N/A	ENSP00000380566.1	P48509

Frequencies

GnomAD3 genomes AF: 0.00344 AC: 523 AN: 151976 Hom.: 2 Cov.: 34

Gnomad AFR AF: 0.00899

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00577

Gnomad ASJ AF: 0.00173

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000626

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.000618

Gnomad OTH AF: 0.00240

GnomAD2 exomes AF: 0.00143 AC: 356 AN: 249352 AF XY: 0.00124

Gnomad AFR exome AF: 0.00982

Gnomad AMR exome AF: 0.00223

Gnomad ASJ exome AF: 0.00131

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000704

Gnomad OTH exome AF: 0.00296

GnomAD4 exome AF: 0.000765 AC: 1117 AN: 1459990 Hom.: 6 Cov.: 34 AF XY: 0.000737 AC XY: 535 AN XY: 726178

African (AFR) AF: 0.0104 AC: 347 AN: 33474

American (AMR) AF: 0.00239 AC: 107 AN: 44702

Ashkenazi Jewish (ASJ) AF: 0.000728 AC: 19 AN: 26110

East Asian (EAS) AF: 0.00 AC: 0 AN: 39686

South Asian (SAS) AF: 0.000568 AC: 49 AN: 86244

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 52218

Middle Eastern (MID) AF: 0.0168 AC: 97 AN: 5762

European-Non Finnish (NFE) AF: 0.000356 AC: 396 AN: 1111446

Other (OTH) AF: 0.00169 AC: 102 AN: 60348

GnomAD4 genome AF: 0.00343 AC: 522 AN: 152094 Hom.: 2 Cov.: 34 AF XY: 0.00342 AC XY: 254 AN XY: 74328

African (AFR) AF: 0.00897 AC: 372 AN: 41490

American (AMR) AF: 0.00576 AC: 88 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.00173 AC: 6 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5160

South Asian (SAS) AF: 0.000627 AC: 3 AN: 4786

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10598

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.000618 AC: 42 AN: 68000

Other (OTH) AF: 0.00238 AC: 5 AN: 2104

Alfa AF: 0.00218 Hom.: 0

Bravo AF: 0.00383

Asia WGS AF: 0.000866 AC: 3 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	2	not provided (2)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	10
DANN	Benign	0.45
PhyloP100		1.9
Mutation Taster		=100/0	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs150709104; hg19: chr11-837436;