rs12162084

Variant names:

• chr16-26638150-G-A
• rs12162084
• ENST00000806412.1:n.67-3655G>A

Your query was ambiguous. Multiple possible variants found:

• chr16-26638150-G-A
• chr16-26638150-G-T

Variant summary

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

The ENST00000806412.1(ENSG00000304809):​n.67-3655G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.158 in 152,140 control chromosomes in the GnomAD database, including 2,085 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 0.16 (2085 hom., cov: 32)
• Consequence: ENSG00000304809 ENST00000806412.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.233
• Publications: 9 publications found

Genes affected

ENSG00000304809 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.329 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000806412.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000304809	ENST00000806412.1		n.67-3655G>A		intron	N/A
	ENSG00000304829	ENST00000806514.1		n.266+3116C>T		intron	N/A
	ENSG00000304829	ENST00000806515.1		n.70+5438C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.158 AC: 24043 AN: 152022 Hom.: 2084 Cov.: 32

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.262

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.0931

Gnomad EAS AF: 0.294

Gnomad SAS AF: 0.344

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.158 AC: 24039 AN: 152140 Hom.: 2085 Cov.: 32 AF XY: 0.159 AC XY: 11810 AN XY: 74382

African (AFR) AF: 0.143 AC: 5936 AN: 41514

American (AMR) AF: 0.109 AC: 1668 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0931 AC: 323 AN: 3468

East Asian (EAS) AF: 0.294 AC: 1513 AN: 5144

South Asian (SAS) AF: 0.343 AC: 1651 AN: 4816

European-Finnish (FIN) AF: 0.124 AC: 1308 AN: 10590

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.163 AC: 11107 AN: 67994

Other (OTH) AF: 0.126 AC: 266 AN: 2114

Alfa AF: 0.128 Hom.: 604

Bravo AF: 0.153

Asia WGS AF: 0.312 AC: 1088 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.23
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs12162084; hg19: chr16-26649471;