rs7137869

Variant names:

• chr12-119551841-A-G
• rs7137869
• ENST00000509470.2:n.418+1707T>C

Variant summary

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

The ENST00000509470.2(PRKAB1-AS1):​n.418+1707T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.191 in 151,776 control chromosomes in the GnomAD database, including 3,226 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 0.19 (3226 hom., cov: 32)
• Consequence: PRKAB1-AS1 ENST00000509470.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00900
• Publications: 9 publications found

Genes affected

PRKAB1-AS1 (HGNC:58183):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.21 is higher than 0.05.

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+1707T>C		intron	N/A
	PRKAB1-AS1	NR_188490.1		n.283+1707T>C		intron	N/A
	PRKAB1-AS1	NR_188492.1		n.283+1707T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PRKAB1-AS1	ENST00000509470.2	TSL:1	n.418+1707T>C		intron	N/A
	PRKAB1-AS1	ENST00000535511.6	TSL:3	n.885+1707T>C		intron	N/A
	PRKAB1-AS1	ENST00000537366.6	TSL:3	n.251+1707T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.191 AC: 28998 AN: 151656 Hom.: 3218 Cov.: 32

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.193

Gnomad AMR AF: 0.147

Gnomad ASJ AF: 0.0984

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.167

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.171

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

GnomAD4 genome AF: 0.191 AC: 29024 AN: 151776 Hom.: 3226 Cov.: 32 AF XY: 0.190 AC XY: 14072 AN XY: 74142

African (AFR) AF: 0.214 AC: 8872 AN: 41490

American (AMR) AF: 0.147 AC: 2247 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.0984 AC: 341 AN: 3466

East Asian (EAS) AF: 0.150 AC: 779 AN: 5188

South Asian (SAS) AF: 0.167 AC: 799 AN: 4776

European-Finnish (FIN) AF: 0.186 AC: 1938 AN: 10436

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.199 AC: 13485 AN: 67846

Other (OTH) AF: 0.170 AC: 357 AN: 2104

Alfa AF: 0.194 Hom.: 10081

Bravo AF: 0.188

Asia WGS AF: 0.154 AC: 533 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	5.1
DANN	Benign	0.68
PhyloP100		0.0090

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7137869;

hg19: chr12-119989646;