rs3016432

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000204971 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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

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

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

Gnomad4 AFR AF: 0.291

Gnomad4 AMR AF: 0.593

Gnomad4 ASJ AF: 0.418

Gnomad4 EAS AF: 0.525

Gnomad4 SAS AF: 0.421

Gnomad4 FIN AF: 0.433

Gnomad4 NFE AF: 0.520

Gnomad4 OTH AF: 0.486

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3016432; hg19: chr11-71897255;