rs6120708

Variant names:

• chr20-34747722-G-A
• rs6120708
• NM_014071.5:c.2793-794C>T

Variant summary

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

The NM_014071.5(NCOA6):​c.2793-794C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.352 in 151,838 control chromosomes in the GnomAD database, including 9,749 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 0.35 (9749 hom., cov: 31)
• Consequence: NCOA6 NM_014071.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.795
• Publications: 13 publications found

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]

ENSG00000286803 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.388 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NCOA6	NM_014071.5	c.2793-794C>T		intron_variant	Intron 9 of 14	ENST00000359003.7	NP_054790.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NCOA6	ENST00000359003.7	c.2793-794C>T		intron_variant	Intron 9 of 14	1	NM_014071.5	ENSP00000351894.2

Frequencies

GnomAD3 genomes AF: 0.353 AC: 53503 AN: 151720 Hom.: 9749 Cov.: 31

Gnomad AFR AF: 0.289

Gnomad AMI AF: 0.373

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.452

Gnomad EAS AF: 0.238

Gnomad SAS AF: 0.372

Gnomad FIN AF: 0.443

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.392

Gnomad OTH AF: 0.361

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

GnomAD4 genome AF: 0.352 AC: 53512 AN: 151838 Hom.: 9749 Cov.: 31 AF XY: 0.354 AC XY: 26242 AN XY: 74190

African (AFR) AF: 0.289 AC: 11967 AN: 41384

American (AMR) AF: 0.293 AC: 4475 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.452 AC: 1567 AN: 3468

East Asian (EAS) AF: 0.238 AC: 1229 AN: 5170

South Asian (SAS) AF: 0.370 AC: 1782 AN: 4814

European-Finnish (FIN) AF: 0.443 AC: 4651 AN: 10488

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.392 AC: 26605 AN: 67918

Other (OTH) AF: 0.364 AC: 770 AN: 2114

Alfa AF: 0.384 Hom.: 5961

Bravo AF: 0.337

Asia WGS AF: 0.313 AC: 1091 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	12
DANN	Benign	0.72
PhyloP100		0.80
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: rs6120708; hg19: chr20-33335526;