rs11879191

Variant names:

• chr19-10402235-G-A
• rs11879191
• NM_007065.4:c.102+1143C>T

Your query was ambiguous. Multiple possible variants found:

• chr19-10402235-G-A
• chr19-10402235-G-C

Variant summary

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

The NM_007065.4(CDC37):​c.102+1143C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.183 in 151,096 control chromosomes in the GnomAD database, including 2,977 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 0.18 (2977 hom., cov: 29)
• Consequence: CDC37 NM_007065.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.819
• Publications: 64 publications found

Genes affected

CDC37 (HGNC:1735): (cell division cycle 37, HSP90 cochaperone) The protein encoded by this gene is highly similar to Cdc 37, a cell division cycle control protein of Sacchromyces cerevisiae. This protein is a molecular chaperone with specific function in cell signal transduction. It has been shown to form complex with Hsp90 and a variety of protein kinases including CDK4, CDK6, SRC, RAF-1, MOK, as well as eIF2 alpha kinases. It is thought to play a critical role in directing Hsp90 to its target kinases. [provided by RefSeq, Jul 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.481 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_007065.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CDC37	NM_007065.4	MANE Select	c.102+1143C>T		intron	N/A	NP_008996.1	Q16543

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CDC37	ENST00000222005.7	TSL:1 MANE Select	c.102+1143C>T		intron	N/A	ENSP00000222005.1	Q16543
	CDC37	ENST00000937013.1		c.102+1143C>T		intron	N/A	ENSP00000607072.1
	CDC37	ENST00000963718.1		c.102+1143C>T		intron	N/A	ENSP00000633777.1

Frequencies

GnomAD3 genomes AF: 0.183 AC: 27646 AN: 150990 Hom.: 2973 Cov.: 29

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.308

Gnomad AMR AF: 0.170

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.497

Gnomad SAS AF: 0.233

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.188

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.193

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

GnomAD4 genome AF: 0.183 AC: 27667 AN: 151096 Hom.: 2977 Cov.: 29 AF XY: 0.182 AC XY: 13390 AN XY: 73696

African (AFR) AF: 0.119 AC: 4890 AN: 41116

American (AMR) AF: 0.170 AC: 2569 AN: 15106

Ashkenazi Jewish (ASJ) AF: 0.232 AC: 805 AN: 3466

East Asian (EAS) AF: 0.497 AC: 2539 AN: 5106

South Asian (SAS) AF: 0.233 AC: 1116 AN: 4788

European-Finnish (FIN) AF: 0.147 AC: 1521 AN: 10330

Middle Eastern (MID) AF: 0.195 AC: 57 AN: 292

European-Non Finnish (NFE) AF: 0.199 AC: 13487 AN: 67880

Other (OTH) AF: 0.192 AC: 403 AN: 2104

Alfa AF: 0.194 Hom.: 5254

Bravo AF: 0.186

Asia WGS AF: 0.333 AC: 1156 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.1
DANN	Benign	0.43
PhyloP100		-0.82
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: rs11879191; hg19: chr19-10512911;