rs722462

Variant names:

• chr14-93803734-C-A
• rs722462

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 0.199 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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.496 AC: 20534 AN: 41360

American (AMR) AF: 0.114 AC: 1751 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.115 AC: 398 AN: 3466

East Asian (EAS) AF: 0.263 AC: 1360 AN: 5166

South Asian (SAS) AF: 0.144 AC: 695 AN: 4810

European-Finnish (FIN) AF: 0.0629 AC: 668 AN: 10614

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.0649 AC: 4409 AN: 67986

Other (OTH) AF: 0.165 AC: 347 AN: 2108

Alfa AF: 0.109 Hom.: 7830

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
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs722462; hg19: chr14-94270080;