NM_000610.4:c.1153+611C>T

Variant names:

• chr11-35202398-C-T
• rs713330
• NM_000610.4:c.1153+611C>T

Variant summary

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

The NM_000610.4(CD44):​c.1153+611C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.742 in 152,074 control chromosomes in the GnomAD database, including 42,618 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 0.74 (42618 hom., cov: 31)
• Consequence: CD44 NM_000610.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.502
• Publications: 14 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 (EAS) allele frequency at 95% confidence interval = 0.906 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.1153+611C>T		intron	N/A	NP_000601.3
	CD44	NM_001440353.1		c.*1481C>T		3_prime_UTR	Exon 8 of 8	NP_001427282.1
	CD44	NM_001440324.1		c.1156+611C>T		intron	N/A	NP_001427253.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD44	ENST00000428726.8	TSL:1 MANE Select	c.1153+611C>T		intron	N/A	ENSP00000398632.2
	CD44	ENST00000415148.6	TSL:1	c.1024+611C>T		intron	N/A	ENSP00000389830.2
	CD44	ENST00000433892.6	TSL:1	c.668-5707C>T		intron	N/A	ENSP00000392331.2

Frequencies

GnomAD3 genomes AF: 0.742 AC: 112696 AN: 151956 Hom.: 42569 Cov.: 31

Gnomad AFR AF: 0.874

Gnomad AMI AF: 0.652

Gnomad AMR AF: 0.685

Gnomad ASJ AF: 0.748

Gnomad EAS AF: 0.928

Gnomad SAS AF: 0.825

Gnomad FIN AF: 0.725

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.657

Gnomad OTH AF: 0.724

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.742 AC: 112802 AN: 152074 Hom.: 42618 Cov.: 31 AF XY: 0.749 AC XY: 55646 AN XY: 74326

African (AFR) AF: 0.874 AC: 36313 AN: 41526

American (AMR) AF: 0.685 AC: 10448 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.748 AC: 2598 AN: 3472

East Asian (EAS) AF: 0.928 AC: 4804 AN: 5178

South Asian (SAS) AF: 0.823 AC: 3959 AN: 4810

European-Finnish (FIN) AF: 0.725 AC: 7655 AN: 10558

Middle Eastern (MID) AF: 0.724 AC: 210 AN: 290

European-Non Finnish (NFE) AF: 0.657 AC: 44685 AN: 67966

Other (OTH) AF: 0.727 AC: 1535 AN: 2112

Alfa AF: 0.688 Hom.: 135540

Bravo AF: 0.744

Asia WGS AF: 0.871 AC: 3025 AN: 3474

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	0.67
PhyloP100		-0.50
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: rs713330; hg19: chr11-35223945;