rs2785173

Variant names:

• chr11-35134185-G-A
• rs2785173
• ENST00000528366.1:n.617-1045C>T

Your query was ambiguous. Multiple possible variants found:

• chr11-35134185-G-A
• chr11-35134185-G-C
• chr11-35134185-G-T

Variant summary

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

The ENST00000528366.1(CD44-DT):​n.617-1045C>T variant causes a intron 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 ENST00000528366.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.264
• Publications: 7 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=-0.95).
• 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 rank	MANE	Protein	UniProt
CD44-DT	NR_120528.1	n.617-1045C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD44-DT	ENST00000528366.1	n.617-1045C>T		intron_variant	Intron 2 of 2	2
CD44-DT	ENST00000841280.1	n.723-1045C>T		intron_variant	Intron 3 of 3

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

African (AFR) AF: 0.391 AC: 16201 AN: 41410

American (AMR) AF: 0.0578 AC: 884 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0556 AC: 193 AN: 3472

East Asian (EAS) AF: 0.106 AC: 548 AN: 5188

South Asian (SAS) AF: 0.142 AC: 684 AN: 4816

European-Finnish (FIN) AF: 0.0111 AC: 117 AN: 10588

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0387 AC: 2631 AN: 67998

Other (OTH) AF: 0.111 AC: 234 AN: 2112

Alfa AF: 0.0770 Hom.: 3519

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
PhyloP100		-0.26
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs2785173; hg19: chr11-35155732;