rs412790

Positions:

• chr14-22552777-G-A

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 0.105 in 152,158 control chromosomes in the GnomAD database, including 906 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 0.11 (906 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.31

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.17 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.105 AC: 15995 AN: 152040 Hom.: 909 Cov.: 31

Gnomad AFR AF: 0.0830

Gnomad AMI AF: 0.0669

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.0723

Gnomad EAS AF: 0.0129

Gnomad SAS AF: 0.0580

Gnomad FIN AF: 0.0966

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.0971

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

GnomAD4 genome AF: 0.105 AC: 15997 AN: 152158 Hom.: 906 Cov.: 31 AF XY: 0.103 AC XY: 7662 AN XY: 74378

Gnomad4 AFR AF: 0.0828

Gnomad4 AMR AF: 0.175

Gnomad4 ASJ AF: 0.0723

Gnomad4 EAS AF: 0.0131

Gnomad4 SAS AF: 0.0580

Gnomad4 FIN AF: 0.0966

Gnomad4 NFE AF: 0.117

Gnomad4 OTH AF: 0.0961

Alfa AF: 0.115 Hom.: 1487

Bravo AF: 0.110

Asia WGS AF: 0.0510 AC: 179 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	9.3
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs412790; hg19: chr14-23021720;