rs11821102

Positions:

• chr11-35230997-G-A

Variant summary

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

The NM_000610.4(CD44):​c.*1664G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0658 in 153,820 control chromosomes in the GnomAD database, including 487 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 0.066 (485 hom., cov: 32)
  • Exomes 𝑓: 0.033 (2 hom.)
• Consequence: CD44 NM_000610.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.39

Genes affected

CD44 (HGNC:1681): (CD44 molecule (IN blood group)) The protein encoded by this gene is a cell-surface glycoprotein involved in cell-cell interactions, cell adhesion and migration. It is a receptor for hyaluronic acid (HA) and can also interact with other ligands, such as osteopontin, collagens, and matrix metalloproteinases (MMPs). This protein participates in a wide variety of cellular functions including lymphocyte activation, recirculation and homing, hematopoiesis, and tumor metastasis. Transcripts for this gene undergo complex alternative splicing that results in many functionally distinct isoforms, however, the full length nature of some of these variants has not been determined. Alternative splicing is the basis for the structural and functional diversity of this protein, and may be related to tumor metastasis. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.137 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CD44	NM_000610.4	c.*1664G>A		3_prime_UTR_variant	18/18	ENST00000428726.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CD44	ENST00000428726.8	c.*1664G>A		3_prime_UTR_variant	18/18	1	NM_000610.4	A2
CD44	ENST00000263398.11	c.*1664G>A		3_prime_UTR_variant	9/9	1		A2

Frequencies

GnomAD3 genomes AF: 0.0661 AC: 10049 AN: 152058 Hom.: 482 Cov.: 32

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.0912

Gnomad AMR AF: 0.0308

Gnomad ASJ AF: 0.0170

Gnomad EAS AF: 0.0819

Gnomad SAS AF: 0.0350

Gnomad FIN AF: 0.0262

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0392

Gnomad OTH AF: 0.0575

GnomAD4 exome AF: 0.0328 AC: 54 AN: 1644 Hom.: 2 Cov.: 0 AF XY: 0.0301 AC XY: 27 AN XY: 898

Gnomad4 AFR exome AF: 0.150

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.0294

Gnomad4 EAS exome AF: 0.100

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.0185

Gnomad4 NFE exome AF: 0.0227

Gnomad4 OTH exome AF: 0.0156

GnomAD4 genome AF: 0.0662 AC: 10067 AN: 152176 Hom.: 485 Cov.: 32 AF XY: 0.0660 AC XY: 4915 AN XY: 74416

Gnomad4 AFR AF: 0.140

Gnomad4 AMR AF: 0.0306

Gnomad4 ASJ AF: 0.0170

Gnomad4 EAS AF: 0.0822

Gnomad4 SAS AF: 0.0345

Gnomad4 FIN AF: 0.0262

Gnomad4 NFE AF: 0.0392

Gnomad4 OTH AF: 0.0569

Alfa AF: 0.0423 Hom.: 202

Bravo AF: 0.0685

Asia WGS AF: 0.0730 AC: 252 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.1
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11821102; hg19: chr11-35252544;