chr22-39109388-T-C

Variant names:

• chr22-39109388-T-C
• rs139336

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 0.539 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.758 AC: 31452 AN: 41508

American (AMR) AF: 0.390 AC: 5957 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.457 AC: 1584 AN: 3468

East Asian (EAS) AF: 0.352 AC: 1817 AN: 5162

South Asian (SAS) AF: 0.476 AC: 2287 AN: 4808

European-Finnish (FIN) AF: 0.536 AC: 5652 AN: 10542

Middle Eastern (MID) AF: 0.466 AC: 137 AN: 294

European-Non Finnish (NFE) AF: 0.464 AC: 31532 AN: 67960

Other (OTH) AF: 0.483 AC: 1021 AN: 2114

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
PhyloP100		0.055

Splicing

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

Other links and lift over

dbSNP: rs139336; hg19: chr22-39505393;