11-35162980-C-T

Variant names:

• chr11-35162980-C-T
• rs353638
• NM_000610.4:c.68-13595C>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.68-13595C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.284 in 151,884 control chromosomes in the GnomAD database, including 6,499 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 0.28 (6499 hom., cov: 32)
• Consequence: CD44 NM_000610.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.483
• Publications: 6 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]

SNORD164 (HGNC:51878): (small nucleolar RNA, C/D box 164)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.386 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CD44	NM_000610.4	c.68-13595C>T		intron_variant	Intron 1 of 17	ENST00000428726.8	NP_000601.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD44	ENST00000428726.8	c.68-13595C>T		intron_variant	Intron 1 of 17	1	NM_000610.4	ENSP00000398632.2

Frequencies

GnomAD3 genomes AF: 0.284 AC: 43046 AN: 151766 Hom.: 6466 Cov.: 32

Gnomad AFR AF: 0.390

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.273

Gnomad ASJ AF: 0.162

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.300

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.243

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.284 AC: 43132 AN: 151884 Hom.: 6499 Cov.: 32 AF XY: 0.285 AC XY: 21141 AN XY: 74228

African (AFR) AF: 0.391 AC: 16160 AN: 41374

American (AMR) AF: 0.273 AC: 4168 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.162 AC: 561 AN: 3466

East Asian (EAS) AF: 0.121 AC: 623 AN: 5168

South Asian (SAS) AF: 0.230 AC: 1111 AN: 4828

European-Finnish (FIN) AF: 0.300 AC: 3159 AN: 10534

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.243 AC: 16477 AN: 67940

Other (OTH) AF: 0.273 AC: 575 AN: 2110

Alfa AF: 0.255 Hom.: 7931

Bravo AF: 0.288

Asia WGS AF: 0.217 AC: 760 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.54
DANN	Benign	0.54
PhyloP100		-0.48
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: rs353638; hg19: chr11-35184527;