rs490361

chr6-125832107-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_181782.5(NCOA7):c.50+16703T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.261 in 152,166 control chromosomes in the GnomAD database, including 6,292 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 0.26 (6292 hom., cov: 32)
• Consequence: NCOA7 NM_181782.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.241

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.42 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NCOA7	NM_181782.5	c.50+16703T>C		intron_variant		ENST00000392477.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NCOA7	ENST00000392477.7	c.50+16703T>C		intron_variant		1	NM_181782.5

Frequencies

GnomAD3 genomes AF: 0.261 AC: 39634 AN: 152048 Hom.: 6286 Cov.: 32

Gnomad AFR AF: 0.0766

Gnomad AMI AF: 0.356

Gnomad AMR AF: 0.414

Gnomad ASJ AF: 0.355

Gnomad EAS AF: 0.222

Gnomad SAS AF: 0.435

Gnomad FIN AF: 0.345

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.309

Gnomad OTH AF: 0.278

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

GnomAD4 genome AF: 0.261 AC: 39648 AN: 152166 Hom.: 6292 Cov.: 32 AF XY: 0.268 AC XY: 19944 AN XY: 74378

Gnomad4 AFR AF: 0.0765

Gnomad4 AMR AF: 0.415

Gnomad4 ASJ AF: 0.355

Gnomad4 EAS AF: 0.222

Gnomad4 SAS AF: 0.435

Gnomad4 FIN AF: 0.345

Gnomad4 NFE AF: 0.309

Gnomad4 OTH AF: 0.275

Alfa AF: 0.300 Hom.: 3897

Bravo AF: 0.256

Asia WGS AF: 0.303 AC: 1055 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	2.2
Dann	Benign	0.45

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

Publications

LitVar

Other links and lift over

dbSNP: rs490361; hg19: chr6-126153253;