9-4699273-G-T

Variant names:

• chr9-4699273-G-T
• rs5022070
• NM_017913.4:c.747+1394G>T

Variant summary

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

The NM_017913.4(CDC37L1):​c.747+1394G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.49 in 151,976 control chromosomes in the GnomAD database, including 21,138 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 0.49 (21138 hom., cov: 32)
• Consequence: CDC37L1 NM_017913.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09
• Publications: 2 publications found

Genes affected

CDC37L1 (HGNC:17179): (cell division cycle 37 like 1, HSP90 cochaperone) CDC37L1 is a cytoplasmic phosphoprotein that exists in complex with HSP90 (HSPCA; MIM 140571) as well as several other proteins involved in HSP90-mediated protein folding (Scholz et al., 2001 [PubMed 11413142]).[supplied by OMIM, Mar 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.772 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_017913.4. 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
	CDC37L1	NM_017913.4	MANE Select	c.747+1394G>T		intron	N/A	NP_060383.2	Q7L3B6

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CDC37L1	ENST00000381854.4	TSL:1 MANE Select	c.747+1394G>T		intron	N/A	ENSP00000371278.3	Q7L3B6
	CDC37L1	ENST00000906225.1		c.687+1394G>T		intron	N/A	ENSP00000576284.1
	CDC37L1	ENST00000381858.5	TSL:5	c.747+1394G>T		intron	N/A	ENSP00000371282.1	B1AL69

Frequencies

GnomAD3 genomes AF: 0.490 AC: 74352 AN: 151856 Hom.: 21097 Cov.: 32

Gnomad AFR AF: 0.779

Gnomad AMI AF: 0.512

Gnomad AMR AF: 0.409

Gnomad ASJ AF: 0.351

Gnomad EAS AF: 0.615

Gnomad SAS AF: 0.522

Gnomad FIN AF: 0.307

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.356

Gnomad OTH AF: 0.455

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

GnomAD4 genome AF: 0.490 AC: 74459 AN: 151976 Hom.: 21138 Cov.: 32 AF XY: 0.486 AC XY: 36060 AN XY: 74268

African (AFR) AF: 0.779 AC: 32328 AN: 41490

American (AMR) AF: 0.409 AC: 6231 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.351 AC: 1216 AN: 3468

East Asian (EAS) AF: 0.615 AC: 3169 AN: 5150

South Asian (SAS) AF: 0.522 AC: 2520 AN: 4824

European-Finnish (FIN) AF: 0.307 AC: 3239 AN: 10552

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.356 AC: 24212 AN: 67930

Other (OTH) AF: 0.455 AC: 961 AN: 2110

Alfa AF: 0.443 Hom.: 2217

Bravo AF: 0.507

Asia WGS AF: 0.572 AC: 1986 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.75
DANN	Benign	0.40
PhyloP100		-1.1
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: rs5022070; hg19: chr9-4699273; COSMIC: COSV67865891;