rs6087619

Variant names:

• chr20-34700707-G-C
• rs6087619
• ENST00000628752.2:c.557-3464C>G

Variant summary

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

The ENST00000628752.2(NCOA6):​c.557-3464C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.356 in 152,096 control chromosomes in the GnomAD database, including 9,908 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 0.36 (9908 hom., cov: 31)
• Consequence: NCOA6 ENST00000628752.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.70

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.394 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NCOA6	ENST00000628752.2	c.557-3464C>G		intron_variant	Intron 5 of 5	5		ENSP00000486894.1
NCOA6	ENST00000434040.5	n.40-1859C>G		intron_variant	Intron 1 of 2	3
NCOA6	ENST00000593786.1	n.568-1859C>G		intron_variant	Intron 1 of 2	5

Frequencies

GnomAD3 genomes AF: 0.356 AC: 54166 AN: 151978 Hom.: 9911 Cov.: 31

Gnomad AFR AF: 0.293

Gnomad AMI AF: 0.372

Gnomad AMR AF: 0.300

Gnomad ASJ AF: 0.453

Gnomad EAS AF: 0.241

Gnomad SAS AF: 0.357

Gnomad FIN AF: 0.443

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.398

Gnomad OTH AF: 0.355

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

GnomAD4 genome AF: 0.356 AC: 54174 AN: 152096 Hom.: 9908 Cov.: 31 AF XY: 0.357 AC XY: 26505 AN XY: 74330

Gnomad4 AFR AF: 0.293

Gnomad4 AMR AF: 0.299

Gnomad4 ASJ AF: 0.453

Gnomad4 EAS AF: 0.240

Gnomad4 SAS AF: 0.355

Gnomad4 FIN AF: 0.443

Gnomad4 NFE AF: 0.398

Gnomad4 OTH AF: 0.358

Alfa AF: 0.390 Hom.: 1486

Bravo AF: 0.342

Asia WGS AF: 0.306 AC: 1066 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.42
DANN	Benign	0.75

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs6087619; hg19: chr20-33288511;