rs12199382

Positions:

• chr6-22326901-G-A
• chr6-22326901-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.305 in 151,958 control chromosomes in the GnomAD database, including 8,655 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 0.30 (8655 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.402 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.22326901G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CASC15	ENST00000561912.3	n.705+9103G>A		intron_variant		5
CASC15	ENST00000651569.1	n.641+9103G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.305 AC: 46264 AN: 151840 Hom.: 8653 Cov.: 33

Gnomad AFR AF: 0.0821

Gnomad AMI AF: 0.379

Gnomad AMR AF: 0.323

Gnomad ASJ AF: 0.355

Gnomad EAS AF: 0.385

Gnomad SAS AF: 0.262

Gnomad FIN AF: 0.452

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.406

Gnomad OTH AF: 0.327

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

GnomAD4 genome AF: 0.305 AC: 46282 AN: 151958 Hom.: 8655 Cov.: 33 AF XY: 0.309 AC XY: 22913 AN XY: 74266

Gnomad4 AFR AF: 0.0819

Gnomad4 AMR AF: 0.323

Gnomad4 ASJ AF: 0.355

Gnomad4 EAS AF: 0.385

Gnomad4 SAS AF: 0.264

Gnomad4 FIN AF: 0.452

Gnomad4 NFE AF: 0.406

Gnomad4 OTH AF: 0.328

Alfa AF: 0.233 Hom.: 932

Bravo AF: 0.285

Asia WGS AF: 0.285 AC: 992 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	0.094
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12199382; hg19: chr6-22327130;