rs3016432

Variant names:

• chr11-72186211-C-T
• rs3016432
• ENST00000378140.3:n.419+12302G>A

Variant summary

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

The ENST00000378140.3(ENSG00000204971):​n.419+12302G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.454 in 151,814 control chromosomes in the GnomAD database, including 16,496 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 0.45 (16496 hom., cov: 30)
• Consequence: ENSG00000204971 ENST00000378140.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.179
• Publications: 11 publications found

Genes affected

ENSG00000204971 (HGNC:58347):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.583 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FOLR1-AS1	NR_199595.1	n.419+12302G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000204971	ENST00000378140.3	n.419+12302G>A		intron_variant	Intron 2 of 2	3
ENSG00000204971	ENST00000824615.1	n.218-22832G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.454 AC: 68849 AN: 151696 Hom.: 16491 Cov.: 30

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.602

Gnomad AMR AF: 0.593

Gnomad ASJ AF: 0.418

Gnomad EAS AF: 0.525

Gnomad SAS AF: 0.422

Gnomad FIN AF: 0.433

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.520

Gnomad OTH AF: 0.492

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

GnomAD4 genome AF: 0.454 AC: 68865 AN: 151814 Hom.: 16496 Cov.: 30 AF XY: 0.450 AC XY: 33392 AN XY: 74190

African (AFR) AF: 0.291 AC: 12030 AN: 41374

American (AMR) AF: 0.593 AC: 9055 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.418 AC: 1446 AN: 3462

East Asian (EAS) AF: 0.525 AC: 2709 AN: 5158

South Asian (SAS) AF: 0.421 AC: 2024 AN: 4802

European-Finnish (FIN) AF: 0.433 AC: 4570 AN: 10548

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.520 AC: 35303 AN: 67900

Other (OTH) AF: 0.486 AC: 1025 AN: 2108

Alfa AF: 0.478 Hom.: 2250

Bravo AF: 0.464

Asia WGS AF: 0.424 AC: 1472 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.8
DANN	Benign	0.58
PhyloP100		0.18

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs3016432; hg19: chr11-71897255;