chr11-35136854-T-C

Position:

• chr11-35136854-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_120528.1(CD44-DT):​n.336-228A>G variant causes a intron, non coding transcript 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 NR_120528.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.220

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CD44-DT	NR_120528.1	n.336-228A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CD44-DT	ENST00000528366.1	n.336-228A>G		intron_variant, non_coding_transcript_variant		2
CD44-DT	ENST00000530263.1	n.30-228A>G		intron_variant, non_coding_transcript_variant		2
CD44-DT	ENST00000661581.2	n.1255-228A>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.192

Gnomad4 AMR AF: 0.387

Gnomad4 ASJ AF: 0.392

Gnomad4 EAS AF: 0.413

Gnomad4 SAS AF: 0.359

Gnomad4 FIN AF: 0.237

Gnomad4 NFE AF: 0.239

Gnomad4 OTH AF: 0.288

Alfa AF: 0.253 Hom.: 6162

Bravo AF: 0.261

Asia WGS AF: 0.362 AC: 1259 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1425802; hg19: chr11-35158401;