2-24682493-C-T

Position:

• chr2-24682493-C-T

Variant summary

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

The NM_003743.5(NCOA1):​c.355-458C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.435 in 152,002 control chromosomes in the GnomAD database, including 15,968 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 0.44 (15968 hom., cov: 31)
• Consequence: NCOA1 NM_003743.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.303

Genes affected

NCOA1 (HGNC:7668): (nuclear receptor coactivator 1) The protein encoded by this gene acts as a transcriptional coactivator for steroid and nuclear hormone receptors. It is a member of the p160/steroid receptor coactivator (SRC) family and like other family members has histone acetyltransferase activity and contains a nuclear localization signal, as well as bHLH and PAS domains. The product of this gene binds nuclear receptors directly and stimulates the transcriptional activities in a hormone-dependent fashion. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.58).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.587 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NCOA1	NM_003743.5	c.355-458C>T		intron_variant		ENST00000348332.8	NP_003734.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NCOA1	ENST00000348332.8	c.355-458C>T		intron_variant		1	NM_003743.5	ENSP00000320940.5

Frequencies

GnomAD3 genomes AF: 0.435 AC: 66120 AN: 151884 Hom.: 15951 Cov.: 31

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.408

Gnomad AMR AF: 0.597

Gnomad ASJ AF: 0.564

Gnomad EAS AF: 0.528

Gnomad SAS AF: 0.533

Gnomad FIN AF: 0.442

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.507

Gnomad OTH AF: 0.466

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

GnomAD4 genome AF: 0.435 AC: 66144 AN: 152002 Hom.: 15968 Cov.: 31 AF XY: 0.437 AC XY: 32492 AN XY: 74286

Gnomad4 AFR AF: 0.222

Gnomad4 AMR AF: 0.597

Gnomad4 ASJ AF: 0.564

Gnomad4 EAS AF: 0.527

Gnomad4 SAS AF: 0.531

Gnomad4 FIN AF: 0.442

Gnomad4 NFE AF: 0.507

Gnomad4 OTH AF: 0.473

Alfa AF: 0.473 Hom.: 3979

Bravo AF: 0.436

Asia WGS AF: 0.549 AC: 1906 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	15
DANN	Benign	0.90

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: rs2053372; hg19: chr2-24905362;