rs6900852

Variant names:

• chr6-125901927-G-A
• rs6900852
• NM_181782.5:c.2096+11117G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-125901927-G-A
• chr6-125901927-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_181782.5(NCOA7):​c.2096+11117G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.491 in 151,898 control chromosomes in the GnomAD database, including 19,266 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 0.49 (19266 hom., cov: 31)
• Consequence: NCOA7 NM_181782.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365
• Publications: 5 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.613 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.2096+11117G>A		intron	N/A	NP_861447.3
	NCOA7	NM_001199619.2		c.2096+11117G>A		intron	N/A	NP_001186548.1
	NCOA7	NM_001199620.2		c.2096+11117G>A		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.2096+11117G>A		intron	N/A	ENSP00000376269.2
	NCOA7	ENST00000368357.7	TSL:1	c.2096+11117G>A		intron	N/A	ENSP00000357341.3
	NCOA7	ENST00000229634.13	TSL:2	c.1751+11117G>A		intron	N/A	ENSP00000229634.9

Frequencies

GnomAD3 genomes AF: 0.491 AC: 74572 AN: 151780 Hom.: 19242 Cov.: 31

Gnomad AFR AF: 0.312

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.623

Gnomad ASJ AF: 0.515

Gnomad EAS AF: 0.526

Gnomad SAS AF: 0.445

Gnomad FIN AF: 0.554

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.562

Gnomad OTH AF: 0.514

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

GnomAD4 genome AF: 0.491 AC: 74643 AN: 151898 Hom.: 19266 Cov.: 31 AF XY: 0.491 AC XY: 36428 AN XY: 74266

African (AFR) AF: 0.312 AC: 12917 AN: 41416

American (AMR) AF: 0.623 AC: 9517 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.515 AC: 1787 AN: 3468

East Asian (EAS) AF: 0.527 AC: 2707 AN: 5136

South Asian (SAS) AF: 0.445 AC: 2142 AN: 4816

European-Finnish (FIN) AF: 0.554 AC: 5845 AN: 10548

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.562 AC: 38164 AN: 67930

Other (OTH) AF: 0.520 AC: 1092 AN: 2102

Alfa AF: 0.524 Hom.: 13343

Bravo AF: 0.491

Asia WGS AF: 0.519 AC: 1803 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.7
DANN	Benign	0.24
PhyloP100		0.36
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: rs6900852; hg19: chr6-126223073;