rs773584572

Variant names:

• chr6-125885334-C-A
• rs773584572
• NM_181782.5:c.875C>A

Your query was ambiguous. Multiple possible variants found:

• chr6-125885334-C-A
• chr6-125885334-C-G
• chr6-125885334-C-T

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_181782.5(NCOA7):​c.875C>A​(p.Ala292Asp) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A292G) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: NCOA7 NM_181782.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.17
• Publications: 0 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: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NCOA7	NM_181782.5	c.875C>A	p.Ala292Asp	missense_variant	Exon 8 of 16	ENST00000392477.7	NP_861447.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NCOA7	ENST00000392477.7	c.875C>A	p.Ala292Asp	missense_variant	Exon 8 of 16	1	NM_181782.5	ENSP00000376269.2
NCOA7	ENST00000368357.7	c.875C>A	p.Ala292Asp	missense_variant	Exon 9 of 17	1		ENSP00000357341.3
NCOA7	ENST00000229634.13	c.563C>A	p.Ala188Asp	missense_variant	Exon 7 of 15	2		ENSP00000229634.9

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.98
BayesDel_addAF	Uncertain	0.16	D
BayesDel_noAF	Uncertain	-0.010
CADD	Pathogenic	28
DANN	Uncertain	1.0
DEOGEN2	Benign	0.041	T;T;.
Eigen	Pathogenic	0.75
Eigen_PC	Pathogenic	0.75
FATHMM_MKL	Pathogenic	0.98	D
LIST_S2	Uncertain	0.87	.;D;D
M_CAP	Benign	0.024	T
MetaRNN	Uncertain	0.57	D;D;D
MetaSVM	Benign	-0.90	T
MutationAssessor	Uncertain	2.6	M;M;.
PhyloP100		6.2
PrimateAI	Pathogenic	0.80	T
PROVEAN	Benign	-2.1	N;N;N
REVEL	Benign	0.20
Sift	Uncertain	0.013	D;D;D
Sift4G	Uncertain	0.020	D;D;D
Polyphen		1.0	D;D;.
Vest4		0.81
MutPred		0.19		Gain of disorder (P = 0.0407);Gain of disorder (P = 0.0407);.;
MVP		0.082
MPC		0.59
ClinPred		0.87	D
GERP RS		5.6
Varity_R		0.34
gMVP		0.89
Mutation Taster		=62/38	polymorphism

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: rs773584572; hg19: chr6-126206480;