rs6798928

Positions:

• chr3-151862085-A-T

Variant summary

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

The NR_110202.1(AADACL2-AS1):​n.319+65772T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.634 in 151,952 control chromosomes in the GnomAD database, including 31,645 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 0.63 (31645 hom., cov: 31)
• Consequence: AADACL2-AS1 NR_110202.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.170

Genes affected

AADACL2-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.797 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
AADACL2-AS1	NR_110202.1	n.319+65772T>A		intron_variant
AADACL2-AS1	NR_110203.1	n.319+65772T>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AADACL2-AS1	ENST00000475855.1	n.319+65772T>A		intron_variant		5
AADACL2-AS1	ENST00000483843.6	n.439+55530T>A		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.634 AC: 96288 AN: 151834 Hom.: 31594 Cov.: 31

Gnomad AFR AF: 0.804

Gnomad AMI AF: 0.520

Gnomad AMR AF: 0.576

Gnomad ASJ AF: 0.578

Gnomad EAS AF: 0.438

Gnomad SAS AF: 0.457

Gnomad FIN AF: 0.500

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.598

Gnomad OTH AF: 0.595

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

GnomAD4 genome AF: 0.634 AC: 96389 AN: 151952 Hom.: 31645 Cov.: 31 AF XY: 0.623 AC XY: 46250 AN XY: 74266

Gnomad4 AFR AF: 0.805

Gnomad4 AMR AF: 0.576

Gnomad4 ASJ AF: 0.578

Gnomad4 EAS AF: 0.437

Gnomad4 SAS AF: 0.455

Gnomad4 FIN AF: 0.500

Gnomad4 NFE AF: 0.598

Gnomad4 OTH AF: 0.595

Alfa AF: 0.600 Hom.: 15312

Bravo AF: 0.647

Asia WGS AF: 0.470 AC: 1633 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.8
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6798928; hg19: chr3-151579873;