rs139998

Variant names:

• chr22-36466454-T-C
• rs139998

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 0.309 in 152,108 control chromosomes in the GnomAD database, including 9,672 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 0.31 (9672 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.04

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.586 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: 0.309 AC: 46904 AN: 151990 Hom.: 9654 Cov.: 33

Gnomad AFR AF: 0.592

Gnomad AMI AF: 0.277

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.290

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.229

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.263

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

GnomAD4 genome AF: 0.309 AC: 46972 AN: 152108 Hom.: 9672 Cov.: 33 AF XY: 0.306 AC XY: 22749 AN XY: 74368

Gnomad4 AFR AF: 0.592

Gnomad4 AMR AF: 0.174

Gnomad4 ASJ AF: 0.290

Gnomad4 EAS AF: 0.138

Gnomad4 SAS AF: 0.236

Gnomad4 FIN AF: 0.229

Gnomad4 NFE AF: 0.199

Gnomad4 OTH AF: 0.263

Alfa AF: 0.211 Hom.: 5213

Bravo AF: 0.313

Asia WGS AF: 0.219 AC: 762 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.0060
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs139998; hg19: chr22-36862501;