rs28566535

Variant names:

• chr15-51308944-A-C
• rs28566535
• NM_000103.4:c.-39+29551T>G

Your query was ambiguous. Multiple possible variants found:

• chr15-51308944-A-C
• chr15-51308944-A-G
• chr15-51308944-A-T

Variant summary

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

The NM_000103.4(CYP19A1):​c.-39+29551T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.198 in 152,014 control chromosomes in the GnomAD database, including 5,906 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 0.20 (5906 hom., cov: 32)
• Consequence: CYP19A1 NM_000103.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.307
• Publications: 14 publications found

Genes affected

CYP19A1 (HGNC:2594): (cytochrome P450 family 19 subfamily A member 1) This gene encodes a member of the cytochrome P450 superfamily of enzymes. The cytochrome P450 proteins are monooxygenases which catalyze many reactions involved in drug metabolism and synthesis of cholesterol, steroids and other lipids. This protein localizes to the endoplasmic reticulum and catalyzes the last steps of estrogen biosynthesis. Mutations in this gene can result in either increased or decreased aromatase activity; the associated phenotypes suggest that estrogen functions both as a sex steroid hormone and in growth or differentiation. Alternative promoter use and alternative splicing results in multiple transcript variants that have different tissue specificities. [provided by RefSeq, Dec 2016]

MIR4713HG (HGNC:53124): (MIR4713 host gene)

LOC124903493 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.488 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000103.4. 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
	CYP19A1	NM_000103.4	MANE Select	c.-39+29551T>G		intron	N/A	NP_000094.2
	CYP19A1	NM_001347248.1		c.-39+14872T>G		intron	N/A	NP_001334177.1
	CYP19A1	NM_001347249.2		c.-39+9489T>G		intron	N/A	NP_001334178.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CYP19A1	ENST00000396402.6	TSL:1 MANE Select	c.-39+29551T>G		intron	N/A	ENSP00000379683.1
	CYP19A1	ENST00000439712.6	TSL:1	n.-283+29551T>G		intron	N/A	ENSP00000390614.2
	CYP19A1	ENST00000557934.5	TSL:1	n.-39+29551T>G		intron	N/A	ENSP00000454004.1

Frequencies

GnomAD3 genomes AF: 0.198 AC: 30027 AN: 151896 Hom.: 5864 Cov.: 32

Gnomad AFR AF: 0.493

Gnomad AMI AF: 0.00440

Gnomad AMR AF: 0.132

Gnomad ASJ AF: 0.0678

Gnomad EAS AF: 0.314

Gnomad SAS AF: 0.265

Gnomad FIN AF: 0.0814

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0487

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.198 AC: 30132 AN: 152014 Hom.: 5906 Cov.: 32 AF XY: 0.200 AC XY: 14895 AN XY: 74318

African (AFR) AF: 0.494 AC: 20448 AN: 41412

American (AMR) AF: 0.133 AC: 2028 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0678 AC: 235 AN: 3468

East Asian (EAS) AF: 0.313 AC: 1622 AN: 5174

South Asian (SAS) AF: 0.263 AC: 1267 AN: 4814

European-Finnish (FIN) AF: 0.0814 AC: 860 AN: 10566

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0487 AC: 3310 AN: 67984

Other (OTH) AF: 0.157 AC: 330 AN: 2108

Alfa AF: 0.0226 Hom.: 15

Bravo AF: 0.213

Asia WGS AF: 0.333 AC: 1158 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.8
DANN	Benign	0.49
PhyloP100		-0.31
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: rs28566535; hg19: chr15-51601141;