rs910871

chr20-34745404-C-A

Variant summary

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

The NM_014071.5(NCOA6):c.2914+1403G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.843 in 152,164 control chromosomes in the GnomAD database, including 54,260 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 0.84 (54260 hom., cov: 31)
• Consequence: NCOA6 NM_014071.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.411

Genes affected

NCOA6 (HGNC:15936): (nuclear receptor coactivator 6) The protein encoded by this gene is a transcriptional coactivator that can interact with nuclear hormone receptors to enhance their transcriptional activator functions. This protein has been shown to be involved in the hormone-dependent coactivation of several receptors, including prostanoid, retinoid, vitamin D3, thyroid hormone, and steroid receptors. Alternatively spliced transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Jun 2011]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.897 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NCOA6	NM_014071.5	c.2914+1403G>T		intron_variant		ENST00000359003.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NCOA6	ENST00000359003.7	c.2914+1403G>T		intron_variant		1	NM_014071.5
	ENST00000655046.1	n.207+3797C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.843 AC: 128149 AN: 152044 Hom.: 54197 Cov.: 31

Gnomad AFR AF: 0.841

Gnomad AMI AF: 0.967

Gnomad AMR AF: 0.910

Gnomad ASJ AF: 0.877

Gnomad EAS AF: 0.769

Gnomad SAS AF: 0.679

Gnomad FIN AF: 0.883

Gnomad MID AF: 0.832

Gnomad NFE AF: 0.836

Gnomad OTH AF: 0.862

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

GnomAD4 genome AF: 0.843 AC: 128272 AN: 152164 Hom.: 54260 Cov.: 31 AF XY: 0.845 AC XY: 62843 AN XY: 74414

Gnomad4 AFR AF: 0.841

Gnomad4 AMR AF: 0.910

Gnomad4 ASJ AF: 0.877

Gnomad4 EAS AF: 0.768

Gnomad4 SAS AF: 0.680

Gnomad4 FIN AF: 0.883

Gnomad4 NFE AF: 0.836

Gnomad4 OTH AF: 0.863

Alfa AF: 0.851 Hom.: 16618

Bravo AF: 0.851

Asia WGS AF: 0.754 AC: 2619 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	3.6
Dann	Benign	0.47

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: rs910871; hg19: chr20-33333208;