chr6-125844319-G-A

Position:

• chr6-125844319-G-A

Variant summary

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

The NM_181782.5(NCOA7):​c.51-10701G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.852 in 152,168 control chromosomes in the GnomAD database, including 55,731 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 0.85 (55731 hom., cov: 32)
• Consequence: NCOA7 NM_181782.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.472

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.917 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NCOA7	NM_181782.5	c.51-10701G>A		intron_variant		ENST00000392477.7	NP_861447.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NCOA7	ENST00000392477.7	c.51-10701G>A		intron_variant		1	NM_181782.5	ENSP00000376269

Frequencies

GnomAD3 genomes AF: 0.852 AC: 129605 AN: 152050 Hom.: 55685 Cov.: 32

Gnomad AFR AF: 0.732

Gnomad AMI AF: 0.888

Gnomad AMR AF: 0.929

Gnomad ASJ AF: 0.953

Gnomad EAS AF: 0.760

Gnomad SAS AF: 0.915

Gnomad FIN AF: 0.909

Gnomad MID AF: 0.902

Gnomad NFE AF: 0.896

Gnomad OTH AF: 0.873

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

GnomAD4 genome AF: 0.852 AC: 129713 AN: 152168 Hom.: 55731 Cov.: 32 AF XY: 0.855 AC XY: 63575 AN XY: 74374

Gnomad4 AFR AF: 0.732

Gnomad4 AMR AF: 0.929

Gnomad4 ASJ AF: 0.953

Gnomad4 EAS AF: 0.760

Gnomad4 SAS AF: 0.915

Gnomad4 FIN AF: 0.909

Gnomad4 NFE AF: 0.896

Gnomad4 OTH AF: 0.873

Alfa AF: 0.896 Hom.: 82001

Bravo AF: 0.847

Asia WGS AF: 0.841 AC: 2921 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	7.7
DANN	Benign	0.72

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: rs481233; hg19: chr6-126165465;