rs12602486

Variant names:

• chr17-44164561-T-G
• rs12602486
• ENST00000755665.1:n.186-7102A>C

Variant summary

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

The ENST00000755665.1(ASB16-AS1):​n.186-7102A>C variant causes a intron change. The variant allele was found at a frequency of 0.0377 in 152,268 control chromosomes in the GnomAD database, including 139 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 0.038 (139 hom., cov: 31)
• Consequence: ASB16-AS1 ENST00000755665.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned
• Publications: 10 publications found

Genes affected

ASB16-AS1 (HGNC:25442): (ASB16 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0627 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000755665.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ASB16-AS1	ENST00000755665.1		n.186-7102A>C		intron	N/A
	ASB16-AS1	ENST00000755666.1		n.236-4855A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0377 AC: 5742 AN: 152150 Hom.: 138 Cov.: 31

Gnomad AFR AF: 0.0370

Gnomad AMI AF: 0.0307

Gnomad AMR AF: 0.0509

Gnomad ASJ AF: 0.0666

Gnomad EAS AF: 0.0684

Gnomad SAS AF: 0.0323

Gnomad FIN AF: 0.0241

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0341

Gnomad OTH AF: 0.0325

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

GnomAD4 genome AF: 0.0377 AC: 5747 AN: 152268 Hom.: 139 Cov.: 31 AF XY: 0.0373 AC XY: 2780 AN XY: 74458

African (AFR) AF: 0.0370 AC: 1537 AN: 41568

American (AMR) AF: 0.0509 AC: 778 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0666 AC: 231 AN: 3470

East Asian (EAS) AF: 0.0686 AC: 355 AN: 5178

South Asian (SAS) AF: 0.0329 AC: 159 AN: 4826

European-Finnish (FIN) AF: 0.0241 AC: 256 AN: 10616

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0341 AC: 2322 AN: 68018

Other (OTH) AF: 0.0317 AC: 67 AN: 2112

Alfa AF: 0.0409 Hom.: 80

Bravo AF: 0.0413

Asia WGS AF: 0.0550 AC: 192 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.48
DANN	Benign	0.31

Splicing

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

Other links and lift over

dbSNP: rs12602486; hg19: chr17-42241929;