rs2785173

Positions:

• chr11-35134185-G-A

Variant summary

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

The NR_120528.1(CD44-DT):​n.617-1045C>T 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 0.142 in 152,080 control chromosomes in the GnomAD database, including 3,383 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 0.14 (3383 hom., cov: 32)
• Consequence: CD44-DT NR_120528.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.264

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=-0.95).
• 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/exons	MANE	Protein	UniProt
CD44-DT	NR_120528.1	n.617-1045C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CD44-DT	ENST00000528366.1	n.617-1045C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.142 AC: 21559 AN: 151964 Hom.: 3375 Cov.: 32

Gnomad AFR AF: 0.391

Gnomad AMI AF: 0.0835

Gnomad AMR AF: 0.0579

Gnomad ASJ AF: 0.0556

Gnomad EAS AF: 0.106

Gnomad SAS AF: 0.142

Gnomad FIN AF: 0.0111

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0387

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.142 AC: 21593 AN: 152080 Hom.: 3383 Cov.: 32 AF XY: 0.137 AC XY: 10216 AN XY: 74366

Gnomad4 AFR AF: 0.391

Gnomad4 AMR AF: 0.0578

Gnomad4 ASJ AF: 0.0556

Gnomad4 EAS AF: 0.106

Gnomad4 SAS AF: 0.142

Gnomad4 FIN AF: 0.0111

Gnomad4 NFE AF: 0.0387

Gnomad4 OTH AF: 0.111

Alfa AF: 0.0702 Hom.: 774

Bravo AF: 0.155

Asia WGS AF: 0.140 AC: 484 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.2
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2785173; hg19: chr11-35155732;