rs139336

Variant names:

• chr22-39109388-T-C
• rs139336

Your query was ambiguous. Multiple possible variants found:

• chr22-39109388-T-C
• chr22-39109388-T-G

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 0.539 in 152,030 control chromosomes in the GnomAD database, including 23,541 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 0.54 (23541 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0550

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.751 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: 0.539 AC: 81840 AN: 151912 Hom.: 23517 Cov.: 32

Gnomad AFR AF: 0.758

Gnomad AMI AF: 0.528

Gnomad AMR AF: 0.391

Gnomad ASJ AF: 0.457

Gnomad EAS AF: 0.352

Gnomad SAS AF: 0.475

Gnomad FIN AF: 0.536

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.464

Gnomad OTH AF: 0.488

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

GnomAD4 genome AF: 0.539 AC: 81917 AN: 152030 Hom.: 23541 Cov.: 32 AF XY: 0.537 AC XY: 39875 AN XY: 74274

Gnomad4 AFR AF: 0.758

Gnomad4 AMR AF: 0.390

Gnomad4 ASJ AF: 0.457

Gnomad4 EAS AF: 0.352

Gnomad4 SAS AF: 0.476

Gnomad4 FIN AF: 0.536

Gnomad4 NFE AF: 0.464

Gnomad4 OTH AF: 0.483

Alfa AF: 0.501 Hom.: 2404

Bravo AF: 0.533

Asia WGS AF: 0.404 AC: 1408 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.0
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs139336; hg19: chr22-39505393;