chr20-34767243-G-A

Variant names:

• chr20-34767243-G-A
• rs4911442
• NM_014071.5:c.514+1221C>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.514+1221C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.927 in 152,304 control chromosomes in the GnomAD database, including 65,670 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 0.93 (65670 hom., cov: 31)
• Consequence: NCOA6 NM_014071.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.890
• Publications: 53 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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NCOA6	NM_014071.5	c.514+1221C>T		intron_variant	Intron 5 of 14	ENST00000359003.7	NP_054790.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NCOA6	ENST00000359003.7	c.514+1221C>T		intron_variant	Intron 5 of 14	1	NM_014071.5	ENSP00000351894.2

Frequencies

GnomAD3 genomes AF: 0.927 AC: 141103 AN: 152186 Hom.: 65610 Cov.: 31

Gnomad AFR AF: 0.979

Gnomad AMI AF: 0.981

Gnomad AMR AF: 0.949

Gnomad ASJ AF: 0.942

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.947

Gnomad FIN AF: 0.931

Gnomad MID AF: 0.934

Gnomad NFE AF: 0.882

Gnomad OTH AF: 0.938

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

GnomAD4 genome AF: 0.927 AC: 141222 AN: 152304 Hom.: 65670 Cov.: 31 AF XY: 0.931 AC XY: 69305 AN XY: 74468

African (AFR) AF: 0.979 AC: 40695 AN: 41578

American (AMR) AF: 0.950 AC: 14528 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.942 AC: 3266 AN: 3468

East Asian (EAS) AF: 0.999 AC: 5183 AN: 5188

South Asian (SAS) AF: 0.947 AC: 4559 AN: 4814

European-Finnish (FIN) AF: 0.931 AC: 9875 AN: 10612

Middle Eastern (MID) AF: 0.929 AC: 273 AN: 294

European-Non Finnish (NFE) AF: 0.882 AC: 59968 AN: 68028

Other (OTH) AF: 0.938 AC: 1980 AN: 2110

Alfa AF: 0.910 Hom.: 55875

Bravo AF: 0.931

Asia WGS AF: 0.977 AC: 3399 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.21
DANN	Benign	0.51
PhyloP100		-0.89
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: rs4911442; hg19: chr20-33355046;