rs1696

Variant names:

• chr17-6941095-G-A
• rs1696
• ENST00000570562.5:n.238-60033C>T

Variant summary

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

The ENST00000570562.5(ALOX12-AS1):​n.238-60033C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.116 in 152,006 control chromosomes in the GnomAD database, including 1,435 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 (1435 hom., cov: 31)
• Consequence: ALOX12-AS1 ENST00000570562.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.598

Genes affected

ALOX12-AS1 (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 (AFR) allele frequency at 95% confidence interval = 0.226 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
ALOX12-AS1	ENST00000570562.5	n.238-60033C>T		intron_variant	Intron 2 of 3	3
ALOX12-AS1	ENST00000572385.5	n.231-60033C>T		intron_variant	Intron 2 of 3	4
ALOX12P2	ENST00000574183.1	n.73-12566G>A		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.116 AC: 17580 AN: 151888 Hom.: 1426 Cov.: 31

Gnomad AFR AF: 0.230

Gnomad AMI AF: 0.0253

Gnomad AMR AF: 0.0831

Gnomad ASJ AF: 0.125

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.0792

Gnomad FIN AF: 0.0560

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.0748

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.116 AC: 17613 AN: 152006 Hom.: 1435 Cov.: 31 AF XY: 0.112 AC XY: 8344 AN XY: 74304

Gnomad4 AFR AF: 0.230

Gnomad4 AMR AF: 0.0831

Gnomad4 ASJ AF: 0.125

Gnomad4 EAS AF: 0.00154

Gnomad4 SAS AF: 0.0793

Gnomad4 FIN AF: 0.0560

Gnomad4 NFE AF: 0.0749

Gnomad4 OTH AF: 0.109

Alfa AF: 0.0883 Hom.: 434

Bravo AF: 0.122

Asia WGS AF: 0.0480 AC: 167 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	1.6
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1696; hg19: chr17-6844414;