chr6-125842453-A-G

Variant names:

• chr6-125842453-A-G
• rs17708107
• NM_181782.5:c.51-12567A>G

Variant summary

Our verdict is Benign. The variant received -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
• 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]

ACMG classification

Our verdict: Benign. The variant received -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.

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NCOA7	NM_181782.5	MANE Select	c.51-12567A>G		intron	N/A	NP_861447.3
	NCOA7	NM_001199619.2		c.51-12567A>G		intron	N/A	NP_001186548.1
	NCOA7	NM_001199620.2		c.51-12567A>G		intron	N/A	NP_001186549.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NCOA7	ENST00000392477.7	TSL:1 MANE Select	c.51-12567A>G		intron	N/A	ENSP00000376269.2
	NCOA7	ENST00000368357.7	TSL:1	c.51-12567A>G		intron	N/A	ENSP00000357341.3
	NCOA7	ENST00000487635.1	TSL:1	n.188-12567A>G		intron	N/A

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

African (AFR) AF: 0.0271 AC: 1126 AN: 41578

American (AMR) AF: 0.0578 AC: 884 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.133 AC: 462 AN: 3470

East Asian (EAS) AF: 0.00115 AC: 6 AN: 5196

South Asian (SAS) AF: 0.0547 AC: 264 AN: 4830

European-Finnish (FIN) AF: 0.0656 AC: 696 AN: 10612

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0955 AC: 6495 AN: 68012

Other (OTH) AF: 0.0639 AC: 135 AN: 2112

Alfa AF: 0.0913 Hom.: 1174

Bravo AF: 0.0629

Asia WGS AF: 0.0340 AC: 120 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.9
DANN	Benign	0.67
PhyloP100		-0.010
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: rs17708107; hg19: chr6-126163599;