chr6-22312733-A-G

Position:

• chr6-22312733-A-G

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 0.309 in 152,122 control chromosomes in the GnomAD database, including 8,924 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 0.31 (8924 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.329

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.409 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.22312733A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CASC15	ENST00000561912.3	n.570-4094A>G		intron_variant		5
CASC15	ENST00000651569.1	n.506-4094A>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.309 AC: 47021 AN: 152004 Hom.: 8924 Cov.: 32

Gnomad AFR AF: 0.0829

Gnomad AMI AF: 0.385

Gnomad AMR AF: 0.331

Gnomad ASJ AF: 0.382

Gnomad EAS AF: 0.389

Gnomad SAS AF: 0.263

Gnomad FIN AF: 0.441

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.413

Gnomad OTH AF: 0.331

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

GnomAD4 genome AF: 0.309 AC: 47038 AN: 152122 Hom.: 8924 Cov.: 32 AF XY: 0.312 AC XY: 23217 AN XY: 74346

Gnomad4 AFR AF: 0.0827

Gnomad4 AMR AF: 0.331

Gnomad4 ASJ AF: 0.382

Gnomad4 EAS AF: 0.389

Gnomad4 SAS AF: 0.266

Gnomad4 FIN AF: 0.441

Gnomad4 NFE AF: 0.414

Gnomad4 OTH AF: 0.332

Alfa AF: 0.355 Hom.: 1329

Bravo AF: 0.292

Asia WGS AF: 0.287 AC: 999 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	3.5
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12525289; hg19: chr6-22312962;