rs17708107

Positions:

• chr6-125842453-A-G

Variant summary

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

The NM_181782.5(NCOA7):​c.51-12567A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0666 in 152,302 control chromosomes in the GnomAD database, including 423 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 0.067 (423 hom., cov: 32)
• Consequence: NCOA7 NM_181782.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0100

Genes affected

NCOA7 (HGNC:21081): (nuclear receptor coactivator 7) Enables nuclear receptor binding activity and nuclear receptor coactivator activity. Involved in positive regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

NCOA7 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0936 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NCOA7	NM_181782.5	c.51-12567A>G		intron_variant		ENST00000392477.7	NP_861447.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NCOA7	ENST00000392477.7	c.51-12567A>G		intron_variant		1	NM_181782.5	ENSP00000376269.2

Frequencies

GnomAD3 genomes AF: 0.0666 AC: 10133 AN: 152184 Hom.: 422 Cov.: 32

Gnomad AFR AF: 0.0269

Gnomad AMI AF: 0.0548

Gnomad AMR AF: 0.0580

Gnomad ASJ AF: 0.133

Gnomad EAS AF: 0.00115

Gnomad SAS AF: 0.0538

Gnomad FIN AF: 0.0656

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0955

Gnomad OTH AF: 0.0656

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

GnomAD4 genome AF: 0.0666 AC: 10141 AN: 152302 Hom.: 423 Cov.: 32 AF XY: 0.0645 AC XY: 4803 AN XY: 74452

Gnomad4 AFR AF: 0.0271

Gnomad4 AMR AF: 0.0578

Gnomad4 ASJ AF: 0.133

Gnomad4 EAS AF: 0.00115

Gnomad4 SAS AF: 0.0547

Gnomad4 FIN AF: 0.0656

Gnomad4 NFE AF: 0.0955

Gnomad4 OTH AF: 0.0639

Alfa AF: 0.0926 Hom.: 955

Bravo AF: 0.0629

Asia WGS AF: 0.0340 AC: 120 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.9
DANN	Benign	0.67

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: rs17708107; hg19: chr6-126163599;