rs12006166

Variant names:

• chr9-115662708-A-T
• rs12006166
• ENST00000644998.2:n.229-20727T>A

Variant summary

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

The ENST00000644998.2(ENSG00000228714):​n.229-20727T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.117 in 151,708 control chromosomes in the GnomAD database, including 1,124 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 0.12 (1124 hom., cov: 32)
• Consequence: ENSG00000228714 ENST00000644998.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.636
• Publications: 5 publications found

Genes affected

ENSG00000228714 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.14 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376235	XR_930270.3	n.145-1676A>T		intron_variant	Intron 2 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000228714	ENST00000644998.2	n.229-20727T>A		intron_variant	Intron 2 of 2
ENSG00000228714	ENST00000645745.1	n.422+26516T>A		intron_variant	Intron 4 of 5
ENSG00000228714	ENST00000646338.1	n.275+78754T>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.118 AC: 17812 AN: 151590 Hom.: 1127 Cov.: 32

Gnomad AFR AF: 0.0788

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.0559

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.156

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.113

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

GnomAD4 genome AF: 0.117 AC: 17814 AN: 151708 Hom.: 1124 Cov.: 32 AF XY: 0.116 AC XY: 8637 AN XY: 74156

African (AFR) AF: 0.0786 AC: 3258 AN: 41442

American (AMR) AF: 0.128 AC: 1939 AN: 15188

Ashkenazi Jewish (ASJ) AF: 0.113 AC: 390 AN: 3460

East Asian (EAS) AF: 0.0554 AC: 286 AN: 5160

South Asian (SAS) AF: 0.149 AC: 716 AN: 4810

European-Finnish (FIN) AF: 0.116 AC: 1228 AN: 10594

Middle Eastern (MID) AF: 0.154 AC: 45 AN: 292

European-Non Finnish (NFE) AF: 0.142 AC: 9591 AN: 67746

Other (OTH) AF: 0.111 AC: 234 AN: 2106

Alfa AF: 0.128 Hom.: 166

Bravo AF: 0.113

Asia WGS AF: 0.111 AC: 388 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.1
DANN	Benign	0.61
PhyloP100		0.64

Splicing

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

Other links and lift over

dbSNP: rs12006166; hg19: chr9-118424987;