rs7972859

Variant names:

• chr12-119552240-C-T
• rs7972859
• ENST00000509470.2:n.418+1308G>A

Variant summary

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

The ENST00000509470.2(ENSG00000248636):​n.418+1308G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.15 in 151,654 control chromosomes in the GnomAD database, including 2,138 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 0.15 (2138 hom., cov: 32)
• Consequence: ENSG00000248636 ENST00000509470.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.230
• Publications: 2 publications found

Genes affected

ENSG00000248636 (HGNC:58183):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.177 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PRKAB1-AS1	NR_188489.1	n.885+1308G>A		intron_variant	Intron 2 of 2
PRKAB1-AS1	NR_188490.1	n.283+1308G>A		intron_variant	Intron 2 of 3
PRKAB1-AS1	NR_188492.1	n.283+1308G>A		intron_variant	Intron 2 of 2
PRKAB1-AS1	NR_188494.1	n.283+1308G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000248636	ENST00000509470.2	n.418+1308G>A		intron_variant	Intron 2 of 2	1
ENSG00000248636	ENST00000535511.6	n.885+1308G>A		intron_variant	Intron 2 of 2	3
ENSG00000248636	ENST00000537366.6	n.251+1308G>A		intron_variant	Intron 2 of 3	3

Frequencies

GnomAD3 genomes AF: 0.150 AC: 22783 AN: 151536 Hom.: 2136 Cov.: 32

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.184

Gnomad AMR AF: 0.126

Gnomad ASJ AF: 0.0919

Gnomad EAS AF: 0.149

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.171

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.180

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.150 AC: 22791 AN: 151654 Hom.: 2138 Cov.: 32 AF XY: 0.149 AC XY: 11045 AN XY: 74062

African (AFR) AF: 0.111 AC: 4627 AN: 41506

American (AMR) AF: 0.125 AC: 1913 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.0919 AC: 318 AN: 3462

East Asian (EAS) AF: 0.149 AC: 771 AN: 5168

South Asian (SAS) AF: 0.155 AC: 736 AN: 4756

European-Finnish (FIN) AF: 0.171 AC: 1783 AN: 10424

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.180 AC: 12172 AN: 67780

Other (OTH) AF: 0.132 AC: 278 AN: 2108

Alfa AF: 0.159 Hom.: 603

Bravo AF: 0.144

Asia WGS AF: 0.134 AC: 466 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	5.2
DANN	Benign	0.84
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs7972859; hg19: chr12-119990045;