6-125795807-A-G

Position:

• chr6-125795807-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.-65+4740A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.394 in 151,970 control chromosomes in the GnomAD database, including 13,709 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 0.39 (13709 hom., cov: 31)
• Consequence: NCOA7 NM_181782.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.140

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.647 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NCOA7	NM_181782.5	c.-65+4740A>G		intron_variant		ENST00000392477.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NCOA7	ENST00000392477.7	c.-65+4740A>G		intron_variant		1	NM_181782.5

Frequencies

GnomAD3 genomes AF: 0.394 AC: 59854 AN: 151852 Hom.: 13692 Cov.: 31

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.369

Gnomad AMR AF: 0.455

Gnomad ASJ AF: 0.378

Gnomad EAS AF: 0.665

Gnomad SAS AF: 0.419

Gnomad FIN AF: 0.453

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.501

Gnomad OTH AF: 0.434

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

GnomAD4 genome AF: 0.394 AC: 59887 AN: 151970 Hom.: 13709 Cov.: 31 AF XY: 0.391 AC XY: 29075 AN XY: 74272

Gnomad4 AFR AF: 0.145

Gnomad4 AMR AF: 0.455

Gnomad4 ASJ AF: 0.378

Gnomad4 EAS AF: 0.665

Gnomad4 SAS AF: 0.418

Gnomad4 FIN AF: 0.453

Gnomad4 NFE AF: 0.501

Gnomad4 OTH AF: 0.439

Alfa AF: 0.448 Hom.: 6905

Bravo AF: 0.390

Asia WGS AF: 0.517 AC: 1796 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	8.3
DANN	Benign	0.86

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: rs9375411; hg19: chr6-126116953;