NM_000103.4:c.297-4162T>C

Variant names:

• chr15-51232095-A-G
• rs2414095
• NM_000103.4:c.297-4162T>C

Variant summary

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

The NM_000103.4(CYP19A1):​c.297-4162T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.69 in 152,030 control chromosomes in the GnomAD database, including 36,510 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 0.69 (36510 hom., cov: 31)
• Consequence: CYP19A1 NM_000103.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.763

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)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.781 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CYP19A1	NM_000103.4	c.297-4162T>C		intron_variant	Intron 3 of 9	ENST00000396402.6	NP_000094.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CYP19A1	ENST00000396402.6	c.297-4162T>C		intron_variant	Intron 3 of 9	1	NM_000103.4	ENSP00000379683.1

Frequencies

GnomAD3 genomes AF: 0.690 AC: 104840 AN: 151912 Hom.: 36469 Cov.: 31

Gnomad AFR AF: 0.788

Gnomad AMI AF: 0.632

Gnomad AMR AF: 0.624

Gnomad ASJ AF: 0.678

Gnomad EAS AF: 0.690

Gnomad SAS AF: 0.747

Gnomad FIN AF: 0.660

Gnomad MID AF: 0.561

Gnomad NFE AF: 0.650

Gnomad OTH AF: 0.643

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

GnomAD4 genome AF: 0.690 AC: 104937 AN: 152030 Hom.: 36510 Cov.: 31 AF XY: 0.691 AC XY: 51331 AN XY: 74298

Gnomad4 AFR AF: 0.788

Gnomad4 AMR AF: 0.623

Gnomad4 ASJ AF: 0.678

Gnomad4 EAS AF: 0.689

Gnomad4 SAS AF: 0.747

Gnomad4 FIN AF: 0.660

Gnomad4 NFE AF: 0.650

Gnomad4 OTH AF: 0.643

Alfa AF: 0.653 Hom.: 55139

Bravo AF: 0.689

Asia WGS AF: 0.694 AC: 2415 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.46
DANN	Benign	0.43

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: rs2414095; hg19: chr15-51524292;