rs6937402

Positions:

• chr6-22224149-T-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.0552 in 152,288 control chromosomes in the GnomAD database, including 238 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 0.055 (238 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.768

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.26).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0597 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.22224149T>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CASC15	ENST00000561912.3	n.200-32225T>G		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.0552 AC: 8397 AN: 152170 Hom.: 238 Cov.: 33

Gnomad AFR AF: 0.0533

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.0368

Gnomad ASJ AF: 0.0216

Gnomad EAS AF: 0.00212

Gnomad SAS AF: 0.0385

Gnomad FIN AF: 0.0857

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0612

Gnomad OTH AF: 0.0589

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

GnomAD4 genome AF: 0.0552 AC: 8403 AN: 152288 Hom.: 238 Cov.: 33 AF XY: 0.0553 AC XY: 4121 AN XY: 74464

Gnomad4 AFR AF: 0.0532

Gnomad4 AMR AF: 0.0367

Gnomad4 ASJ AF: 0.0216

Gnomad4 EAS AF: 0.00212

Gnomad4 SAS AF: 0.0387

Gnomad4 FIN AF: 0.0857

Gnomad4 NFE AF: 0.0612

Gnomad4 OTH AF: 0.0587

Alfa AF: 0.0568 Hom.: 330

Bravo AF: 0.0513

Asia WGS AF: 0.0220 AC: 75 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.26
CADD	Benign	15
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6937402; hg19: chr6-22224378;