rs1918416

Variant names:

• chr12-119562608-C-T
• rs1918416
• ENST00000509470.2:n.321-8963G>A

Variant summary

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

The ENST00000509470.2(ENSG00000248636):​n.321-8963G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.243 in 152,020 control chromosomes in the GnomAD database, including 5,182 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 0.24 (5182 hom., cov: 31)
• Consequence: ENSG00000248636 ENST00000509470.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0410
• Publications: 5 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.529 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PRKAB1-AS1	NR_188489.1	n.788-8963G>A		intron_variant	Intron 1 of 2
PRKAB1-AS1	NR_188490.1	n.186-8963G>A		intron_variant	Intron 1 of 3
PRKAB1-AS1	NR_188492.1	n.186-8963G>A		intron_variant	Intron 1 of 2
PRKAB1-AS1	NR_188494.1	n.186-8963G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000248636	ENST00000509470.2	n.321-8963G>A		intron_variant	Intron 1 of 2	1
ENSG00000248636	ENST00000535511.6	n.788-8963G>A		intron_variant	Intron 1 of 2	3
ENSG00000248636	ENST00000537366.6	n.154-8963G>A		intron_variant	Intron 1 of 3	3

Frequencies

GnomAD3 genomes AF: 0.243 AC: 36859 AN: 151902 Hom.: 5173 Cov.: 31

Gnomad AFR AF: 0.339

Gnomad AMI AF: 0.180

Gnomad AMR AF: 0.256

Gnomad ASJ AF: 0.239

Gnomad EAS AF: 0.546

Gnomad SAS AF: 0.343

Gnomad FIN AF: 0.171

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.243 AC: 36904 AN: 152020 Hom.: 5182 Cov.: 31 AF XY: 0.245 AC XY: 18174 AN XY: 74310

African (AFR) AF: 0.340 AC: 14071 AN: 41446

American (AMR) AF: 0.256 AC: 3914 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.239 AC: 831 AN: 3470

East Asian (EAS) AF: 0.545 AC: 2813 AN: 5158

South Asian (SAS) AF: 0.344 AC: 1653 AN: 4810

European-Finnish (FIN) AF: 0.171 AC: 1811 AN: 10574

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.163 AC: 11106 AN: 67976

Other (OTH) AF: 0.223 AC: 470 AN: 2110

Alfa AF: 0.190 Hom.: 3089

Bravo AF: 0.254

Asia WGS AF: 0.424 AC: 1471 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.3
DANN	Benign	0.59
PhyloP100		0.041

Splicing

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

Other links and lift over

dbSNP: rs1918416; hg19: chr12-120000413;