rs1195138637

Variant names:

• chr6-125855102-A-G
• rs1195138637
• NM_181782.5:c.133A>G

Your query was ambiguous. Multiple possible variants found:

• chr6-125855102-A-G
• chr6-125855102-A-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_181782.5(NCOA7):​c.133A>G​(p.Asn45Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 16/22 in silico tools predict a benign outcome for this variant. 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. N45Y) 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: 1.33
• 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.03402576).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NCOA7	NM_181782.5	c.133A>G	p.Asn45Asp	missense_variant	Exon 3 of 16	ENST00000392477.7	NP_861447.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NCOA7	ENST00000392477.7	c.133A>G	p.Asn45Asp	missense_variant	Exon 3 of 16	1	NM_181782.5	ENSP00000376269.2

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	Benign	0.073
BayesDel_addAF	Benign	-0.30	T
BayesDel_noAF	Benign	-0.67
CADD	Benign	8.1
DANN	Benign	0.89
DEOGEN2	Benign	0.0035	T;T;.;T;.;T
Eigen	Benign	-0.95
Eigen_PC	Benign	-0.87
FATHMM_MKL	Benign	0.022	N
LIST_S2	Benign	0.28	.;T;.;T;T;T
M_CAP	Benign	0.0054	T
MetaRNN	Benign	0.034	T;T;T;T;T;T
MetaSVM	Benign	-0.94	T
MutationAssessor	Benign	0.34	N;N;.;.;.;.
PhyloP100		1.3
PrimateAI	Benign	0.27	T
PROVEAN	Benign	-0.23	N;N;N;N;N;N
REVEL	Benign	0.059
Sift	Benign	0.13	T;T;T;T;T;T
Sift4G	Benign	0.60	T;T;T;T;T;T
Polyphen		0.0	B;B;.;.;.;.
Vest4		0.13
MutPred		0.075		Loss of methylation at K42 (P = 0.086);Loss of methylation at K42 (P = 0.086);Loss of methylation at K42 (P = 0.086);Loss of methylation at K42 (P = 0.086);Loss of methylation at K42 (P = 0.086);Loss of methylation at K42 (P = 0.086);
MVP		0.043
MPC		0.10
ClinPred		0.030	T
GERP RS		2.4
Varity_R		0.044
gMVP		0.083
Mutation Taster		=98/2	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: rs1195138637; hg19: chr6-126176248;