20-47540255-G-T

Variant names:

• chr20-47540255-G-T
• rs2425955
• NM_181659.3:c.-99+38236G>T

Variant summary

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

The NM_181659.3(NCOA3):​c.-99+38236G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.464 in 151,962 control chromosomes in the GnomAD database, including 16,923 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 0.46 (16923 hom., cov: 31)
• Consequence: NCOA3 NM_181659.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.626
• Publications: 1 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.549 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NCOA3	NM_181659.3	c.-99+38236G>T		intron_variant	Intron 1 of 22	ENST00000371998.8	NP_858045.1
NCOA3	NM_001174087.2	c.-99+38236G>T		intron_variant	Intron 1 of 22		NP_001167558.1
NCOA3	NM_006534.4	c.-99+38236G>T		intron_variant	Intron 1 of 22		NP_006525.2
NCOA3	NM_001174088.2	c.-99+38236G>T		intron_variant	Intron 1 of 22		NP_001167559.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NCOA3	ENST00000371998.8	c.-99+38236G>T		intron_variant	Intron 1 of 22	1	NM_181659.3	ENSP00000361066.3
NCOA3	ENST00000372004.7	c.-99+38236G>T		intron_variant	Intron 1 of 22	1		ENSP00000361073.1
NCOA3	ENST00000371997.3	c.-99+38236G>T		intron_variant	Intron 1 of 22	1		ENSP00000361065.3

Frequencies

GnomAD3 genomes AF: 0.464 AC: 70513 AN: 151844 Hom.: 16899 Cov.: 31

Gnomad AFR AF: 0.554

Gnomad AMI AF: 0.581

Gnomad AMR AF: 0.388

Gnomad ASJ AF: 0.595

Gnomad EAS AF: 0.329

Gnomad SAS AF: 0.391

Gnomad FIN AF: 0.317

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.455

Gnomad OTH AF: 0.494

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

GnomAD4 genome AF: 0.464 AC: 70581 AN: 151962 Hom.: 16923 Cov.: 31 AF XY: 0.457 AC XY: 33933 AN XY: 74262

African (AFR) AF: 0.555 AC: 22978 AN: 41412

American (AMR) AF: 0.387 AC: 5909 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.595 AC: 2064 AN: 3470

East Asian (EAS) AF: 0.329 AC: 1700 AN: 5164

South Asian (SAS) AF: 0.390 AC: 1883 AN: 4832

European-Finnish (FIN) AF: 0.317 AC: 3343 AN: 10546

Middle Eastern (MID) AF: 0.605 AC: 178 AN: 294

European-Non Finnish (NFE) AF: 0.456 AC: 30960 AN: 67960

Other (OTH) AF: 0.492 AC: 1038 AN: 2108

Alfa AF: 0.373 Hom.: 1489

Bravo AF: 0.472

Asia WGS AF: 0.369 AC: 1287 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	4.7
DANN	Benign	0.67
PhyloP100		0.63
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: rs2425955; hg19: chr20-46168999;