rs722462

Variant names:

• chr14-93803734-C-A
• rs722462

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 0.199 in 152,018 control chromosomes in the GnomAD database, including 5,646 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 0.20 (5646 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.565

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.491 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: 0.199 AC: 30237 AN: 151900 Hom.: 5622 Cov.: 32

Gnomad AFR AF: 0.496

Gnomad AMI AF: 0.0945

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.263

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.0629

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.0649

Gnomad OTH AF: 0.166

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

GnomAD4 genome AF: 0.199 AC: 30304 AN: 152018 Hom.: 5646 Cov.: 32 AF XY: 0.197 AC XY: 14644 AN XY: 74302

Gnomad4 AFR AF: 0.496

Gnomad4 AMR AF: 0.114

Gnomad4 ASJ AF: 0.115

Gnomad4 EAS AF: 0.263

Gnomad4 SAS AF: 0.144

Gnomad4 FIN AF: 0.0629

Gnomad4 NFE AF: 0.0649

Gnomad4 OTH AF: 0.165

Alfa AF: 0.0851 Hom.: 1467

Bravo AF: 0.217

Asia WGS AF: 0.214 AC: 745 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.24
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs722462; hg19: chr14-94270080;