rs708891

Variant names:

• chr12-119543772-T-A
• rs708891
• ENST00000509470.2:n.418+9776A>T

Your query was ambiguous. Multiple possible variants found:

• chr12-119543772-T-A
• chr12-119543772-T-C
• chr12-119543772-T-G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000509470.2(PRKAB1-AS1):​n.418+9776A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
• Consequence: PRKAB1-AS1 ENST00000509470.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0750
• Publications: 5 publications found

Genes affected

PRKAB1-AS1 (HGNC:58183):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000509470.2. 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
	PRKAB1-AS1	NR_188489.1		n.885+9776A>T		intron	N/A
	PRKAB1-AS1	NR_188490.1		n.283+9776A>T		intron	N/A
	PRKAB1-AS1	NR_188492.1		n.283+9776A>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PRKAB1-AS1	ENST00000509470.2	TSL:1	n.418+9776A>T		intron	N/A
	PRKAB1-AS1	ENST00000535511.6	TSL:3	n.885+9776A>T		intron	N/A
	PRKAB1-AS1	ENST00000537366.6	TSL:3	n.251+9776A>T		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 31

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

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	9.1
DANN	Benign	0.84
PhyloP100		-0.075

Splicing

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

Other links and lift over

dbSNP: rs708891; hg19: chr12-119981577;