rs11622883

chr14-94689439-T-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 0.372 in 152,150 control chromosomes in the GnomAD database, including 11,204 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 0.37 (11204 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.111

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.449 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.372 AC: 56547 AN: 152030 Hom.: 11203 Cov.: 34

Gnomad AFR AF: 0.275

Gnomad AMI AF: 0.423

Gnomad AMR AF: 0.295

Gnomad ASJ AF: 0.470

Gnomad EAS AF: 0.227

Gnomad SAS AF: 0.361

Gnomad FIN AF: 0.377

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.453

Gnomad OTH AF: 0.381

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

GnomAD4 genome AF: 0.372 AC: 56564 AN: 152150 Hom.: 11204 Cov.: 34 AF XY: 0.367 AC XY: 27263 AN XY: 74370

Gnomad4 AFR AF: 0.275

Gnomad4 AMR AF: 0.295

Gnomad4 ASJ AF: 0.470

Gnomad4 EAS AF: 0.228

Gnomad4 SAS AF: 0.360

Gnomad4 FIN AF: 0.377

Gnomad4 NFE AF: 0.453

Gnomad4 OTH AF: 0.378

Alfa AF: 0.407 Hom.: 1621

Bravo AF: 0.360

Asia WGS AF: 0.265 AC: 924 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	5.8
Dann	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11622883; hg19: chr14-95155776;