rs12711490

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 23 publications found

Genes affected

ENSG00000285163 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000645383.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285163	ENST00000645383.1		n.394-5994T>C		intron	N/A
	ENSG00000285163	ENST00000646214.1		n.78-5994T>C		intron	N/A
	ENSG00000285163	ENST00000646986.2		n.715+3411T>C		intron	N/A

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

African (AFR) AF: 0.0970 AC: 4025 AN: 41484

American (AMR) AF: 0.203 AC: 3100 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0917 AC: 318 AN: 3466

East Asian (EAS) AF: 0.0888 AC: 460 AN: 5180

South Asian (SAS) AF: 0.0742 AC: 358 AN: 4828

European-Finnish (FIN) AF: 0.283 AC: 2990 AN: 10562

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.225 AC: 15272 AN: 67990

Other (OTH) AF: 0.159 AC: 336 AN: 2116

Alfa AF: 0.203 Hom.: 6918

Bravo AF: 0.170

Asia WGS AF: 0.0970 AC: 336 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.1
DANN	Benign	0.58
PhyloP100		-0.095

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs12711490;

hg19: chr16-85973028;