chr6-125901927-G-A

Position:

• chr6-125901927-G-A

Variant summary

Our verdict is Benign. Variant got -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

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=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.613 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NCOA7	NM_181782.5	c.2096+11117G>A		intron_variant		ENST00000392477.7	NP_861447.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NCOA7	ENST00000392477.7	c.2096+11117G>A		intron_variant		1	NM_181782.5	ENSP00000376269
NCOA7	ENST00000368357.7	c.2096+11117G>A		intron_variant		1		ENSP00000357341
NCOA7	ENST00000229634.13	c.1751+11117G>A		intron_variant		2		ENSP00000229634
NCOA7	ENST00000433571.2	n.113+1906G>A		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.312

Gnomad4 AMR AF: 0.623

Gnomad4 ASJ AF: 0.515

Gnomad4 EAS AF: 0.527

Gnomad4 SAS AF: 0.445

Gnomad4 FIN AF: 0.554

Gnomad4 NFE AF: 0.562

Gnomad4 OTH AF: 0.520

Alfa AF: 0.519 Hom.: 8449

Bravo AF: 0.491

Asia WGS AF: 0.519 AC: 1803 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.7
DANN	Benign	0.24

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: rs6900852; hg19: chr6-126223073;