rs11607862

chr11-35223027-C-T

Variant summary

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

The ENST00000442151.6(CD44):c.*649C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.282 in 984,292 control chromosomes in the GnomAD database, including 40,828 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 0.24 (5520 hom., cov: 32)
  • Exomes 𝑓: 0.29 (35308 hom.)
• Consequence: CD44 ENST00000442151.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.822

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=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.474 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CD44	NM_000610.4	c.2024+1295C>T		intron_variant		ENST00000428726.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CD44	ENST00000428726.8	c.2024+1295C>T		intron_variant		1	NM_000610.4	A2

Frequencies

GnomAD3 genomes AF: 0.245 AC: 37200 AN: 151970 Hom.: 5524 Cov.: 32

Gnomad AFR AF: 0.0785

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.270

Gnomad ASJ AF: 0.339

Gnomad EAS AF: 0.358

Gnomad SAS AF: 0.489

Gnomad FIN AF: 0.300

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.299

Gnomad OTH AF: 0.256

GnomAD4 exome AF: 0.289 AC: 240176 AN: 832206 Hom.: 35308 Cov.: 30 AF XY: 0.290 AC XY: 111337 AN XY: 384288

Gnomad4 AFR exome AF: 0.0566

Gnomad4 AMR exome AF: 0.289

Gnomad4 ASJ exome AF: 0.337

Gnomad4 EAS exome AF: 0.350

Gnomad4 SAS exome AF: 0.466

Gnomad4 FIN exome AF: 0.297

Gnomad4 NFE exome AF: 0.289

Gnomad4 OTH exome AF: 0.299

GnomAD4 genome AF: 0.245 AC: 37202 AN: 152086 Hom.: 5520 Cov.: 32 AF XY: 0.251 AC XY: 18675 AN XY: 74334

Gnomad4 AFR AF: 0.0786

Gnomad4 AMR AF: 0.269

Gnomad4 ASJ AF: 0.339

Gnomad4 EAS AF: 0.358

Gnomad4 SAS AF: 0.491

Gnomad4 FIN AF: 0.300

Gnomad4 NFE AF: 0.299

Gnomad4 OTH AF: 0.255

Alfa AF: 0.292 Hom.: 9801

Bravo AF: 0.232

Asia WGS AF: 0.364 AC: 1264 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	1.6
Dann	Benign	0.36

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: rs11607862; hg19: chr11-35244574;