rs12466917

Variant names:

• chr2-206854160-G-A
• rs12466917
• ENST00000438070.2:n.348-9236G>A

Your query was ambiguous. Multiple possible variants found:

• chr2-206854160-G-A
• chr2-206854160-G-T

Variant summary

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

The ENST00000438070.2(ENSG00000229321):​n.348-9236G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 152,060 control chromosomes in the GnomAD database, including 983 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 0.11 (983 hom., cov: 32)
• Consequence: ENSG00000229321 ENST00000438070.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.158

Genes affected

ENSG00000229321 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.126 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
ENSG00000229321	ENST00000438070.2	n.348-9236G>A		intron_variant	Intron 2 of 4	3
ENSG00000229321	ENST00000658291.1	n.3035-9236G>A		intron_variant	Intron 2 of 3
ENSG00000229321	ENST00000658889.1	n.2974-25223G>A		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.111 AC: 16850 AN: 151942 Hom.: 980 Cov.: 32

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.0548

Gnomad AMR AF: 0.0970

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.115

Gnomad FIN AF: 0.0880

Gnomad MID AF: 0.0796

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.111 AC: 16860 AN: 152060 Hom.: 983 Cov.: 32 AF XY: 0.109 AC XY: 8126 AN XY: 74318

Gnomad4 AFR AF: 0.129

Gnomad4 AMR AF: 0.0971

Gnomad4 ASJ AF: 0.114

Gnomad4 EAS AF: 0.109

Gnomad4 SAS AF: 0.115

Gnomad4 FIN AF: 0.0880

Gnomad4 NFE AF: 0.107

Gnomad4 OTH AF: 0.117

Alfa AF: 0.0853 Hom.: 222

Bravo AF: 0.111

Asia WGS AF: 0.110 AC: 386 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.8
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12466917; hg19: chr2-207718884;