chr6-125844319-G-A

Variant names:

• chr6-125844319-G-A
• rs481233
• NM_181782.5:c.51-10701G>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.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
• Publications: 2 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=-0.93).
• 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 rank	MANE	Protein	UniProt
NCOA7	NM_181782.5	c.51-10701G>A		intron_variant	Intron 2 of 15	ENST00000392477.7	NP_861447.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NCOA7	ENST00000392477.7	c.51-10701G>A		intron_variant	Intron 2 of 15	1	NM_181782.5	ENSP00000376269.2

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

African (AFR) AF: 0.732 AC: 30357 AN: 41464

American (AMR) AF: 0.929 AC: 14204 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.953 AC: 3309 AN: 3472

East Asian (EAS) AF: 0.760 AC: 3932 AN: 5174

South Asian (SAS) AF: 0.915 AC: 4420 AN: 4830

European-Finnish (FIN) AF: 0.909 AC: 9633 AN: 10600

Middle Eastern (MID) AF: 0.905 AC: 266 AN: 294

European-Non Finnish (NFE) AF: 0.896 AC: 60936 AN: 68024

Other (OTH) AF: 0.873 AC: 1846 AN: 2114

Alfa AF: 0.890 Hom.: 102785

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
PhyloP100		0.47
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: rs481233; hg19: chr6-126165465;