11-35136854-T-C

Variant names:

• chr11-35136854-T-C
• rs1425802
• ENST00000528366.1:n.336-228A>G

Variant summary

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

The ENST00000528366.1(CD44-DT):​n.336-228A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.255 in 152,000 control chromosomes in the GnomAD database, including 5,423 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 0.25 (5423 hom., cov: 32)
• Consequence: CD44-DT ENST00000528366.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.220
• Publications: 20 publications found

Genes affected

CD44-DT (HGNC:56175): (CD44 divergent transcript)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.398 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000528366.1. 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-DT	NR_120528.1		n.336-228A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD44-DT	ENST00000528366.1	TSL:2	n.336-228A>G		intron	N/A
	CD44-DT	ENST00000530263.2	TSL:2	n.373-228A>G		intron	N/A
	CD44-DT	ENST00000661581.3		n.1260-228A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.254 AC: 38632 AN: 151882 Hom.: 5409 Cov.: 32

Gnomad AFR AF: 0.192

Gnomad AMI AF: 0.136

Gnomad AMR AF: 0.386

Gnomad ASJ AF: 0.392

Gnomad EAS AF: 0.413

Gnomad SAS AF: 0.360

Gnomad FIN AF: 0.237

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.287

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

GnomAD4 genome AF: 0.255 AC: 38691 AN: 152000 Hom.: 5423 Cov.: 32 AF XY: 0.262 AC XY: 19479 AN XY: 74286

African (AFR) AF: 0.192 AC: 7972 AN: 41454

American (AMR) AF: 0.387 AC: 5905 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.392 AC: 1359 AN: 3470

East Asian (EAS) AF: 0.413 AC: 2126 AN: 5150

South Asian (SAS) AF: 0.359 AC: 1727 AN: 4808

European-Finnish (FIN) AF: 0.237 AC: 2503 AN: 10570

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.239 AC: 16271 AN: 67962

Other (OTH) AF: 0.288 AC: 609 AN: 2112

Alfa AF: 0.253 Hom.: 7970

Bravo AF: 0.261

Asia WGS AF: 0.362 AC: 1259 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.9
DANN	Benign	0.53
PhyloP100		0.22

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1425802; hg19: chr11-35158401;