rs11967627

Positions:

• chr6-125801418-A-G

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NCOA7	NM_181782.5	c.-65+10351A>G		intron_variant		ENST00000392477.7
NCOA7-AS1	NR_126386.1	n.191+885T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NCOA7	ENST00000392477.7	c.-65+10351A>G		intron_variant		1	NM_181782.5
NCOA7-AS1	ENST00000429007.1	n.191+885T>C		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.0957

Gnomad4 AMR AF: 0.0696

Gnomad4 ASJ AF: 0.117

Gnomad4 EAS AF: 0.00135

Gnomad4 SAS AF: 0.0414

Gnomad4 FIN AF: 0.141

Gnomad4 NFE AF: 0.0987

Gnomad4 OTH AF: 0.0907

Alfa AF: 0.0986 Hom.: 991

Bravo AF: 0.0899

Asia WGS AF: 0.0360 AC: 123 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.41
DANN	Benign	0.46

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: rs11967627; hg19: chr6-126122564; COSMIC: COSV57659579;