rs11622883

Variant names:

• chr14-94689439-T-A
• rs11622883

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 0.372 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
• Publications: 16 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.275 AC: 11417 AN: 41514

American (AMR) AF: 0.295 AC: 4501 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.470 AC: 1631 AN: 3472

East Asian (EAS) AF: 0.228 AC: 1178 AN: 5176

South Asian (SAS) AF: 0.360 AC: 1737 AN: 4824

European-Finnish (FIN) AF: 0.377 AC: 3982 AN: 10570

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.453 AC: 30806 AN: 68000

Other (OTH) AF: 0.378 AC: 797 AN: 2110

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
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs11622883; hg19: chr14-95155776;