17-22503227-A-G

Variant names:

• chr17-22503227-A-G
• rs7406339

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 0.486 in 151,944 control chromosomes in the GnomAD database, including 18,194 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 0.49 (18194 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.583 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: 0.486 AC: 73829 AN: 151828 Hom.: 18163 Cov.: 32

Gnomad AFR AF: 0.529

Gnomad AMI AF: 0.434

Gnomad AMR AF: 0.521

Gnomad ASJ AF: 0.381

Gnomad EAS AF: 0.600

Gnomad SAS AF: 0.458

Gnomad FIN AF: 0.409

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.464

Gnomad OTH AF: 0.476

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

GnomAD4 genome AF: 0.486 AC: 73906 AN: 151944 Hom.: 18194 Cov.: 32 AF XY: 0.484 AC XY: 35962 AN XY: 74246

African (AFR) AF: 0.530 AC: 21943 AN: 41438

American (AMR) AF: 0.521 AC: 7962 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.381 AC: 1322 AN: 3470

East Asian (EAS) AF: 0.600 AC: 3096 AN: 5158

South Asian (SAS) AF: 0.458 AC: 2201 AN: 4806

European-Finnish (FIN) AF: 0.409 AC: 4313 AN: 10536

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.464 AC: 31552 AN: 67956

Other (OTH) AF: 0.473 AC: 996 AN: 2104

Alfa AF: 0.471 Hom.: 58814

Bravo AF: 0.497

Asia WGS AF: 0.458 AC: 1593 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	4.8
DANN	Benign	0.54
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs7406339; hg19: chr17-22002556;