rs16964211

chr15-51238298-G-Achr15-51238298-G-T

Variant summary

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

The NM_000103.4(CYP19A1):c.146-1289C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.14 in 152,176 control chromosomes in the GnomAD database, including 2,533 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 0.14 (2533 hom., cov: 32)
• Consequence: CYP19A1 NM_000103.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0690

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=-0.74).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.301 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CYP19A1	NM_000103.4	c.146-1289C>T		intron_variant		ENST00000396402.6
MIR4713HG	NR_146310.1	n.195-39685G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CYP19A1	ENST00000396402.6	c.146-1289C>T		intron_variant		1	NM_000103.4	P1
MIR4713HG	ENST00000559909.1	n.195-39685G>A		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.140 AC: 21252 AN: 152058 Hom.: 2526 Cov.: 32

Gnomad AFR AF: 0.306

Gnomad AMI AF: 0.0340

Gnomad AMR AF: 0.0820

Gnomad ASJ AF: 0.0790

Gnomad EAS AF: 0.253

Gnomad SAS AF: 0.268

Gnomad FIN AF: 0.0786

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0498

Gnomad OTH AF: 0.0946

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

GnomAD4 genome AF: 0.140 AC: 21296 AN: 152176 Hom.: 2533 Cov.: 32 AF XY: 0.144 AC XY: 10682 AN XY: 74390

Gnomad4 AFR AF: 0.306

Gnomad4 AMR AF: 0.0817

Gnomad4 ASJ AF: 0.0790

Gnomad4 EAS AF: 0.253

Gnomad4 SAS AF: 0.267

Gnomad4 FIN AF: 0.0786

Gnomad4 NFE AF: 0.0498

Gnomad4 OTH AF: 0.102

Alfa AF: 0.0727 Hom.: 484

Bravo AF: 0.144

Asia WGS AF: 0.302 AC: 1049 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
Cadd	Benign	13
Dann	Benign	0.69

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: rs16964211; hg19: chr15-51530495;