rs139323

chr22-39105473-A-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 151,914 control chromosomes in the GnomAD database, including 23,587 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 (23587 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.669

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.753 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: 0.539 AC: 81850 AN: 151796 Hom.: 23559 Cov.: 31

Gnomad AFR AF: 0.760

Gnomad AMI AF: 0.524

Gnomad AMR AF: 0.391

Gnomad ASJ AF: 0.456

Gnomad EAS AF: 0.354

Gnomad SAS AF: 0.476

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: 81932 AN: 151914 Hom.: 23587 Cov.: 31 AF XY: 0.537 AC XY: 39902 AN XY: 74262

Gnomad4 AFR AF: 0.760

Gnomad4 AMR AF: 0.390

Gnomad4 ASJ AF: 0.456

Gnomad4 EAS AF: 0.355

Gnomad4 SAS AF: 0.476

Gnomad4 FIN AF: 0.536

Gnomad4 NFE AF: 0.464

Gnomad4 OTH AF: 0.483

Alfa AF: 0.513 Hom.: 2635

Bravo AF: 0.534

Asia WGS AF: 0.406 AC: 1418 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	2.2
Dann	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs139323; hg19: chr22-39501478;