rs11967627

Variant names:

• chr6-125801418-A-G
• rs11967627
• NM_181782.5:c.-65+10351A>G

Variant summary

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

The NM_181782.5(NCOA7):​c.-65+10351A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0935 in 152,244 control chromosomes in the GnomAD database, including 681 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 0.094 (681 hom., cov: 32)
• Consequence: NCOA7 NM_181782.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.316
• Publications: 7 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]

NCOA7-AS1 (HGNC:40954): (NCOA7 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0967 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.-65+10351A>G		intron	N/A	NP_861447.3
	NCOA7	NM_001199619.2		c.-64-13873A>G		intron	N/A	NP_001186548.1
	NCOA7	NM_001199620.2		c.-65+4621A>G		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.-65+10351A>G		intron	N/A	ENSP00000376269.2
	NCOA7	ENST00000368357.7	TSL:1	c.-64-13873A>G		intron	N/A	ENSP00000357341.3
	NCOA7	ENST00000229634.13	TSL:2	c.-156+10351A>G		intron	N/A	ENSP00000229634.9

Frequencies

GnomAD3 genomes AF: 0.0936 AC: 14237 AN: 152126 Hom.: 681 Cov.: 32

Gnomad AFR AF: 0.0958

Gnomad AMI AF: 0.168

Gnomad AMR AF: 0.0697

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0416

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.0987

Gnomad OTH AF: 0.0917

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

GnomAD4 genome AF: 0.0935 AC: 14242 AN: 152244 Hom.: 681 Cov.: 32 AF XY: 0.0951 AC XY: 7082 AN XY: 74442

African (AFR) AF: 0.0957 AC: 3975 AN: 41534

American (AMR) AF: 0.0696 AC: 1064 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.117 AC: 407 AN: 3470

East Asian (EAS) AF: 0.00135 AC: 7 AN: 5188

South Asian (SAS) AF: 0.0414 AC: 200 AN: 4826

European-Finnish (FIN) AF: 0.141 AC: 1489 AN: 10596

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.0987 AC: 6712 AN: 68016

Other (OTH) AF: 0.0907 AC: 192 AN: 2116

Alfa AF: 0.0969 Hom.: 1422

Bravo AF: 0.0899

Asia WGS AF: 0.0360 AC: 123 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.41
DANN	Benign	0.46
PhyloP100		-0.32
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: rs11967627; hg19: chr6-126122564; COSMIC: COSV57659579;