6-125813790-G-A

Variant names:

• chr6-125813790-G-A
• rs549438
• NM_181782.5:c.-64-1501G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_181782.5(NCOA7):​c.-64-1501G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.587 in 151,932 control chromosomes in the GnomAD database, including 30,475 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 0.59 (30475 hom., cov: 31)
• Consequence: NCOA7 NM_181782.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0320
• Publications: 3 publications found

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-AS1 (HGNC:40954): (NCOA7 antisense RNA 1)

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 = 0.852 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_181782.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NCOA7	NM_181782.5	MANE Select	c.-64-1501G>A		intron	N/A	NP_861447.3
	NCOA7	NM_001199619.2		c.-64-1501G>A		intron	N/A	NP_001186548.1	Q8NI08-1
	NCOA7	NM_001199620.2		c.-64-1501G>A		intron	N/A	NP_001186549.1	Q8NI08-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NCOA7	ENST00000392477.7	TSL:1 MANE Select	c.-64-1501G>A		intron	N/A	ENSP00000376269.2	Q8NI08-1
	NCOA7	ENST00000368357.7	TSL:1	c.-64-1501G>A		intron	N/A	ENSP00000357341.3	Q8NI08-1
	NCOA7	ENST00000867852.1		c.-64-1501G>A		intron	N/A	ENSP00000537911.1

Frequencies

GnomAD3 genomes AF: 0.587 AC: 89109 AN: 151814 Hom.: 30467 Cov.: 31

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.656

Gnomad AMR AF: 0.760

Gnomad ASJ AF: 0.679

Gnomad EAS AF: 0.873

Gnomad SAS AF: 0.817

Gnomad FIN AF: 0.736

Gnomad MID AF: 0.634

Gnomad NFE AF: 0.712

Gnomad OTH AF: 0.641

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

GnomAD4 genome AF: 0.587 AC: 89131 AN: 151932 Hom.: 30475 Cov.: 31 AF XY: 0.595 AC XY: 44162 AN XY: 74276

African (AFR) AF: 0.203 AC: 8404 AN: 41414

American (AMR) AF: 0.761 AC: 11616 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.679 AC: 2357 AN: 3470

East Asian (EAS) AF: 0.873 AC: 4517 AN: 5174

South Asian (SAS) AF: 0.817 AC: 3932 AN: 4814

European-Finnish (FIN) AF: 0.736 AC: 7763 AN: 10542

Middle Eastern (MID) AF: 0.623 AC: 182 AN: 292

European-Non Finnish (NFE) AF: 0.712 AC: 48404 AN: 67936

Other (OTH) AF: 0.645 AC: 1359 AN: 2108

Alfa AF: 0.682 Hom.: 61138

Bravo AF: 0.572

Asia WGS AF: 0.791 AC: 2747 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.74
DANN	Benign	0.64
PhyloP100		-0.032
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: rs549438; hg19: chr6-126134936;