rs412790

Variant names:

• chr14-22552777-G-A
• rs412790

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.0828 AC: 3437 AN: 41514

American (AMR) AF: 0.175 AC: 2681 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0723 AC: 251 AN: 3470

East Asian (EAS) AF: 0.0131 AC: 68 AN: 5184

South Asian (SAS) AF: 0.0580 AC: 280 AN: 4826

European-Finnish (FIN) AF: 0.0966 AC: 1022 AN: 10580

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.117 AC: 7975 AN: 67984

Other (OTH) AF: 0.0961 AC: 203 AN: 2112

Alfa AF: 0.115 Hom.: 2037

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
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs412790; hg19: chr14-23021720;