rs7310266

Variant names:

• chr12-119660604-T-C
• rs7310266
• ENST00000537366.6:n.153+7339A>G

Variant summary

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

The ENST00000537366.6(ENSG00000248636):​n.153+7339A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.356 in 152,114 control chromosomes in the GnomAD database, including 11,144 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 0.36 (11144 hom., cov: 32)
• Consequence: ENSG00000248636 ENST00000537366.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.893
• Publications: 11 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.561 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PRKAB1-AS1	NR_188490.1	n.185+7339A>G		intron_variant	Intron 1 of 3
PRKAB1-AS1	NR_188492.1	n.185+7339A>G		intron_variant	Intron 1 of 2
PRKAB1-AS1	NR_188494.1	n.185+7339A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000248636	ENST00000537366.6	n.153+7339A>G		intron_variant	Intron 1 of 3	3
ENSG00000248636	ENST00000815425.1	n.566+7339A>G		intron_variant	Intron 1 of 2
ENSG00000248636	ENST00000815426.1	n.182+7339A>G		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.356 AC: 54048 AN: 151996 Hom.: 11130 Cov.: 32

Gnomad AFR AF: 0.568

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.262

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.0142

Gnomad SAS AF: 0.190

Gnomad FIN AF: 0.237

Gnomad MID AF: 0.357

Gnomad NFE AF: 0.311

Gnomad OTH AF: 0.332

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

GnomAD4 genome AF: 0.356 AC: 54103 AN: 152114 Hom.: 11144 Cov.: 32 AF XY: 0.346 AC XY: 25709 AN XY: 74382

African (AFR) AF: 0.567 AC: 23512 AN: 41446

American (AMR) AF: 0.262 AC: 4013 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.276 AC: 956 AN: 3466

East Asian (EAS) AF: 0.0143 AC: 74 AN: 5188

South Asian (SAS) AF: 0.190 AC: 919 AN: 4830

European-Finnish (FIN) AF: 0.237 AC: 2506 AN: 10574

Middle Eastern (MID) AF: 0.356 AC: 104 AN: 292

European-Non Finnish (NFE) AF: 0.311 AC: 21182 AN: 68002

Other (OTH) AF: 0.327 AC: 691 AN: 2110

Alfa AF: 0.325 Hom.: 14331

Bravo AF: 0.365

Asia WGS AF: 0.144 AC: 506 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.6
DANN	Benign	0.60
PhyloP100		-0.89

Splicing

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

Other links and lift over

dbSNP: rs7310266; hg19: chr12-120098409;