rs12711490

Variant names:

• chr16-85939422-T-C
• rs12711490
• ENST00000645383.1:n.394-5994T>C

Variant summary

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

The ENST00000645383.1(ENSG00000285163):​n.394-5994T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.178 in 152,108 control chromosomes in the GnomAD database, including 2,802 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 0.18 (2802 hom., cov: 32)
• Consequence: ENSG00000285163 ENST00000645383.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0950

Genes affected

ENSG00000285163 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.222 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
ENSG00000285163	ENST00000645383.1	n.394-5994T>C		intron_variant	Intron 1 of 3
ENSG00000285163	ENST00000646214.1	n.78-5994T>C		intron_variant	Intron 1 of 3
ENSG00000285163	ENST00000646986.1	n.715+3411T>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.178 AC: 27039 AN: 151990 Hom.: 2801 Cov.: 32

Gnomad AFR AF: 0.0972

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.0917

Gnomad EAS AF: 0.0886

Gnomad SAS AF: 0.0739

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.160

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

GnomAD4 genome AF: 0.178 AC: 27052 AN: 152108 Hom.: 2802 Cov.: 32 AF XY: 0.177 AC XY: 13178 AN XY: 74356

Gnomad4 AFR AF: 0.0970

Gnomad4 AMR AF: 0.203

Gnomad4 ASJ AF: 0.0917

Gnomad4 EAS AF: 0.0888

Gnomad4 SAS AF: 0.0742

Gnomad4 FIN AF: 0.283

Gnomad4 NFE AF: 0.225

Gnomad4 OTH AF: 0.159

Alfa AF: 0.200 Hom.: 1692

Bravo AF: 0.170

Asia WGS AF: 0.0970 AC: 336 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.1
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: rs12711490; hg19: chr16-85973028;