20-47579861-G-T

Position:

• chr20-47579861-G-T

Variant summary

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

The NM_181659.3(NCOA3):​c.-98-3322G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0525 in 152,240 control chromosomes in the GnomAD database, including 952 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 0.053 (952 hom., cov: 32)
• Consequence: NCOA3 NM_181659.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365

Genes affected

NCOA3 (HGNC:7670): (nuclear receptor coactivator 3) The protein encoded by this gene is a nuclear receptor coactivator that interacts with nuclear hormone receptors to enhance their transcriptional activator functions. The encoded protein has histone acetyltransferase activity and recruits p300/CBP-associated factor and CREB binding protein as part of a multisubunit coactivation complex. This protein is initially found in the cytoplasm but is translocated into the nucleus upon phosphorylation. Several transcript variants encoding different isoforms have been found for this gene. In addition, a polymorphic repeat region is found in the C-terminus of the encoded protein. [provided by RefSeq, Mar 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.385 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NCOA3	NM_181659.3	c.-98-3322G>T		intron_variant		ENST00000371998.8	NP_858045.1
NCOA3	NM_001174087.2	c.-98-3322G>T		intron_variant			NP_001167558.1
NCOA3	NM_001174088.2	c.-98-3322G>T		intron_variant			NP_001167559.1
NCOA3	NM_006534.4	c.-98-3322G>T		intron_variant			NP_006525.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NCOA3	ENST00000371998.8	c.-98-3322G>T		intron_variant		1	NM_181659.3	ENSP00000361066	P4
NCOA3	ENST00000371997.3	c.-98-3322G>T		intron_variant		1		ENSP00000361065	A2
NCOA3	ENST00000372004.7	c.-98-3322G>T		intron_variant		1		ENSP00000361073	A2

Frequencies

GnomAD3 genomes AF: 0.0526 AC: 7995 AN: 152122 Hom.: 951 Cov.: 32

Gnomad AFR AF: 0.0255

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.00893

Gnomad EAS AF: 0.400

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.0546

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.00516

Gnomad OTH AF: 0.0550

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

GnomAD4 genome AF: 0.0525 AC: 7996 AN: 152240 Hom.: 952 Cov.: 32 AF XY: 0.0601 AC XY: 4474 AN XY: 74438

Gnomad4 AFR AF: 0.0254

Gnomad4 AMR AF: 0.211

Gnomad4 ASJ AF: 0.00893

Gnomad4 EAS AF: 0.399

Gnomad4 SAS AF: 0.117

Gnomad4 FIN AF: 0.0546

Gnomad4 NFE AF: 0.00516

Gnomad4 OTH AF: 0.0530

Alfa AF: 0.0254 Hom.: 536

Bravo AF: 0.0678

Asia WGS AF: 0.232 AC: 805 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.52
DANN	Benign	0.21

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

Publications

LitVar

Other links and lift over

dbSNP: rs6125048; hg19: chr20-46208605;