rs2425752

Variant names:

• chr20-46073481-T-C
• rs2425752
• NM_020967.3:c.39-2945A>G

Your query was ambiguous. Multiple possible variants found:

• chr20-46073481-T-C
• chr20-46073481-T-G

Variant summary

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

The NM_020967.3(NCOA5):​c.39-2945A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.79 in 152,194 control chromosomes in the GnomAD database, including 48,323 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 0.79 (48323 hom., cov: 32)
• Consequence: NCOA5 NM_020967.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.853
• Publications: 64 publications found

Genes affected

NCOA5 (HGNC:15909): (nuclear receptor coactivator 5) This gene encodes a coregulator for the alpha and beta estrogen receptors and the orphan nuclear receptor NR1D2. The protein localizes to the nucleus, and is thought to have both coactivator and corepressor functions. Its interaction with nuclear receptors is independent of the AF2 domain on the receptors, which is known to regulate interaction with other coreceptors. Several alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jan 2017]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.939 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020967.3. 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
	NCOA5	NM_020967.3	MANE Select	c.39-2945A>G		intron	N/A	NP_066018.1	Q9HCD5
	NCOA5	NM_001348148.2		c.-277-2945A>G		intron	N/A	NP_001335077.1
	NCOA5	NM_001348149.2		c.39-2945A>G		intron	N/A	NP_001335078.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NCOA5	ENST00000290231.11	TSL:1 MANE Select	c.39-2945A>G		intron	N/A	ENSP00000290231.6	Q9HCD5
	NCOA5	ENST00000870777.1		c.39-2945A>G		intron	N/A	ENSP00000540836.1
	NCOA5	ENST00000934594.1		c.39-2945A>G		intron	N/A	ENSP00000604653.1

Frequencies

GnomAD3 genomes AF: 0.790 AC: 120175 AN: 152076 Hom.: 48255 Cov.: 32

Gnomad AFR AF: 0.947

Gnomad AMI AF: 0.761

Gnomad AMR AF: 0.774

Gnomad ASJ AF: 0.704

Gnomad EAS AF: 0.630

Gnomad SAS AF: 0.757

Gnomad FIN AF: 0.710

Gnomad MID AF: 0.742

Gnomad NFE AF: 0.731

Gnomad OTH AF: 0.769

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

GnomAD4 genome AF: 0.790 AC: 120304 AN: 152194 Hom.: 48323 Cov.: 32 AF XY: 0.785 AC XY: 58438 AN XY: 74400

African (AFR) AF: 0.947 AC: 39362 AN: 41570

American (AMR) AF: 0.775 AC: 11846 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.704 AC: 2442 AN: 3470

East Asian (EAS) AF: 0.630 AC: 3259 AN: 5172

South Asian (SAS) AF: 0.756 AC: 3642 AN: 4818

European-Finnish (FIN) AF: 0.710 AC: 7497 AN: 10558

Middle Eastern (MID) AF: 0.743 AC: 217 AN: 292

European-Non Finnish (NFE) AF: 0.731 AC: 49717 AN: 68002

Other (OTH) AF: 0.772 AC: 1628 AN: 2110

Alfa AF: 0.756 Hom.: 103874

Bravo AF: 0.803

Asia WGS AF: 0.756 AC: 2630 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
DANN	Benign	0.65
PhyloP100		-0.85
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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2425752; hg19: chr20-44702120;