rs9897850

chr17-6995799-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NR_040089.1(ALOX12-AS1):n.234-10259G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.481 in 152,072 control chromosomes in the GnomAD database, including 17,749 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.48 (17749 hom., cov: 33)
• Consequence: ALOX12-AS1 NR_040089.1 intron, non_coding_transcript
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.206

Genes affected

ALOX12-AS1 (HGNC:51342): (ALOX12 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BP6: Variant 17-6995799-C-T is Benign according to our data. Variant chr17-6995799-C-T is described in ClinVar as [Benign]. Clinvar id is 1269983.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.502 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ALOX12-AS1	NR_040089.1	n.234-10259G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ALOX12-AS1	ENST00000653385.1	n.139+16397G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.481 AC: 73083 AN: 151954 Hom.: 17730 Cov.: 33

Gnomad AFR AF: 0.475

Gnomad AMI AF: 0.464

Gnomad AMR AF: 0.397

Gnomad ASJ AF: 0.478

Gnomad EAS AF: 0.395

Gnomad SAS AF: 0.491

Gnomad FIN AF: 0.501

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.506

Gnomad OTH AF: 0.484

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

GnomAD4 genome AF: 0.481 AC: 73142 AN: 152072 Hom.: 17749 Cov.: 33 AF XY: 0.479 AC XY: 35631 AN XY: 74328

Gnomad4 AFR AF: 0.475

Gnomad4 AMR AF: 0.396

Gnomad4 ASJ AF: 0.478

Gnomad4 EAS AF: 0.396

Gnomad4 SAS AF: 0.492

Gnomad4 FIN AF: 0.501

Gnomad4 NFE AF: 0.506

Gnomad4 OTH AF: 0.483

Alfa AF: 0.491 Hom.: 2439

Bravo AF: 0.466

Asia WGS AF: 0.435 AC: 1519 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 10, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
Cadd	Benign	7.7
Dann	Benign	0.77
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9897850; hg19: chr17-6899118;