rs11607862

Variant names:

• chr11-35223027-C-T
• rs11607862
• ENST00000442151.6:c.*649C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001202557.2(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 NM_001202557.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.822
• Publications: 13 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001202557.2. 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
	CD44	NM_000610.4	MANE Select	c.2024+1295C>T		intron	N/A	NP_000601.3
	CD44	NM_001202557.2		c.*649C>T		3_prime_UTR	Exon 9 of 9	NP_001189486.1
	CD44	NM_001440324.1		c.2027+1295C>T		intron	N/A	NP_001427253.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD44	ENST00000442151.6	TSL:1	c.*649C>T		3_prime_UTR	Exon 9 of 9	ENSP00000398099.2
	CD44	ENST00000428726.8	TSL:1 MANE Select	c.2024+1295C>T		intron	N/A	ENSP00000398632.2
	CD44	ENST00000415148.6	TSL:1	c.1895+1295C>T		intron	N/A	ENSP00000389830.2

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

African (AFR) AF: 0.0566 AC: 894 AN: 15782

American (AMR) AF: 0.289 AC: 284 AN: 984

Ashkenazi Jewish (ASJ) AF: 0.337 AC: 1737 AN: 5150

East Asian (EAS) AF: 0.350 AC: 1267 AN: 3620

South Asian (SAS) AF: 0.466 AC: 7660 AN: 16438

European-Finnish (FIN) AF: 0.297 AC: 82 AN: 276

Middle Eastern (MID) AF: 0.291 AC: 469 AN: 1614

European-Non Finnish (NFE) AF: 0.289 AC: 219633 AN: 761072

Other (OTH) AF: 0.299 AC: 8150 AN: 27270

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

African (AFR) AF: 0.0786 AC: 3263 AN: 41530

American (AMR) AF: 0.269 AC: 4115 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.339 AC: 1177 AN: 3470

East Asian (EAS) AF: 0.358 AC: 1851 AN: 5168

South Asian (SAS) AF: 0.491 AC: 2361 AN: 4810

European-Finnish (FIN) AF: 0.300 AC: 3164 AN: 10554

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.299 AC: 20334 AN: 67970

Other (OTH) AF: 0.255 AC: 538 AN: 2112

Alfa AF: 0.274 Hom.: 13905

Bravo AF: 0.232

Asia WGS AF: 0.364 AC: 1264 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.6
DANN	Benign	0.36
PhyloP100		-0.82
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs11607862; hg19: chr11-35244574;