rs187116

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_000610.4(CD44):​c.67+4883G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.549 in 152,090 control chromosomes in the GnomAD database, including 24,654 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 0.55 ( 24654 hom., cov: 32)

Consequence

CD44
NM_000610.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0400
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

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 = 0.766 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CD44NM_000610.4 linkuse as main transcriptc.67+4883G>A intron_variant ENST00000428726.8 NP_000601.3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CD44ENST00000428726.8 linkuse as main transcriptc.67+4883G>A intron_variant 1 NM_000610.4 ENSP00000398632 A2P16070-1

Frequencies

GnomAD3 genomes
AF:
0.549
AC:
83442
AN:
151970
Hom.:
24593
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.773
Gnomad AMI
AF:
0.437
Gnomad AMR
AF:
0.501
Gnomad ASJ
AF:
0.452
Gnomad EAS
AF:
0.388
Gnomad SAS
AF:
0.514
Gnomad FIN
AF:
0.367
Gnomad MID
AF:
0.522
Gnomad NFE
AF:
0.474
Gnomad OTH
AF:
0.537
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.549
AC:
83568
AN:
152090
Hom.:
24654
Cov.:
32
AF XY:
0.543
AC XY:
40396
AN XY:
74356
show subpopulations
Gnomad4 AFR
AF:
0.773
Gnomad4 AMR
AF:
0.502
Gnomad4 ASJ
AF:
0.452
Gnomad4 EAS
AF:
0.388
Gnomad4 SAS
AF:
0.515
Gnomad4 FIN
AF:
0.367
Gnomad4 NFE
AF:
0.474
Gnomad4 OTH
AF:
0.540
Alfa
AF:
0.496
Hom.:
16272
Bravo
AF:
0.566
Asia WGS
AF:
0.458
AC:
1591
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
4.1
DANN
Benign
0.69

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs187116; hg19: chr11-35165800; API