chr22-39075909-G-A

Variant names:

• chr22-39075909-G-A
• rs6519165

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 0.474 in 151,990 control chromosomes in the GnomAD database, including 20,190 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 0.47 (20190 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.01
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.712 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: 0.474 AC: 71995 AN: 151872 Hom.: 20183 Cov.: 31

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.523

Gnomad AMR AF: 0.638

Gnomad ASJ AF: 0.584

Gnomad EAS AF: 0.732

Gnomad SAS AF: 0.589

Gnomad FIN AF: 0.514

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.591

Gnomad OTH AF: 0.540

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

GnomAD4 genome AF: 0.474 AC: 71998 AN: 151990 Hom.: 20190 Cov.: 31 AF XY: 0.477 AC XY: 35381 AN XY: 74248

African (AFR) AF: 0.150 AC: 6236 AN: 41480

American (AMR) AF: 0.638 AC: 9738 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.584 AC: 2028 AN: 3470

East Asian (EAS) AF: 0.732 AC: 3774 AN: 5158

South Asian (SAS) AF: 0.588 AC: 2827 AN: 4804

European-Finnish (FIN) AF: 0.514 AC: 5417 AN: 10540

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.591 AC: 40190 AN: 67966

Other (OTH) AF: 0.544 AC: 1149 AN: 2112

Alfa AF: 0.517 Hom.: 2805

Bravo AF: 0.471

Asia WGS AF: 0.666 AC: 2313 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	0.50
DANN	Benign	0.50
PhyloP100		-2.0
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs6519165; hg19: chr22-39471914;