11-35144253-G-A

Variant names:

• chr11-35144253-G-A
• rs187116
• NM_000610.4:c.67+4883G>A

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0400
• Publications: 23 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=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.766 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000610.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD44	NM_000610.4	MANE Select	c.67+4883G>A		intron	N/A	NP_000601.3
	CD44	NM_001440324.1		c.67+4883G>A		intron	N/A	NP_001427253.1
	CD44	NM_001440325.1		c.67+4883G>A		intron	N/A	NP_001427254.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD44	ENST00000428726.8	TSL:1 MANE Select	c.67+4883G>A		intron	N/A	ENSP00000398632.2
	CD44	ENST00000415148.6	TSL:1	c.67+4883G>A		intron	N/A	ENSP00000389830.2
	CD44	ENST00000433892.6	TSL:1	c.67+4883G>A		intron	N/A	ENSP00000392331.2

Frequencies

GnomAD3 genomes AF: 0.549 AC: 83442 AN: 151970 Hom.: 24593 Cov.: 32

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

African (AFR) AF: 0.773 AC: 32077 AN: 41502

American (AMR) AF: 0.502 AC: 7675 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.452 AC: 1569 AN: 3470

East Asian (EAS) AF: 0.388 AC: 2008 AN: 5172

South Asian (SAS) AF: 0.515 AC: 2480 AN: 4820

European-Finnish (FIN) AF: 0.367 AC: 3877 AN: 10560

Middle Eastern (MID) AF: 0.534 AC: 157 AN: 294

European-Non Finnish (NFE) AF: 0.474 AC: 32185 AN: 67954

Other (OTH) AF: 0.540 AC: 1142 AN: 2116

Alfa AF: 0.508 Hom.: 22736

Bravo AF: 0.566

Asia WGS AF: 0.458 AC: 1591 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.1
DANN	Benign	0.69
PhyloP100		0.040
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: rs187116; hg19: chr11-35165800;