17-42390483-G-A

Variant names:

• chr17-42390483-G-A
• rs17405722

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 0.0611 in 152,096 control chromosomes in the GnomAD database, including 344 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 0.061 (344 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.522
• Publications: 23 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0726 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0609 AC: 9256 AN: 151978 Hom.: 338 Cov.: 32

Gnomad AFR AF: 0.0374

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.0477

Gnomad ASJ AF: 0.0446

Gnomad EAS AF: 0.0177

Gnomad SAS AF: 0.0730

Gnomad FIN AF: 0.102

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0743

Gnomad OTH AF: 0.0525

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

GnomAD4 genome AF: 0.0611 AC: 9287 AN: 152096 Hom.: 344 Cov.: 32 AF XY: 0.0614 AC XY: 4560 AN XY: 74326

African (AFR) AF: 0.0377 AC: 1563 AN: 41490

American (AMR) AF: 0.0476 AC: 727 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.0446 AC: 155 AN: 3472

East Asian (EAS) AF: 0.0178 AC: 92 AN: 5176

South Asian (SAS) AF: 0.0730 AC: 352 AN: 4820

European-Finnish (FIN) AF: 0.102 AC: 1078 AN: 10550

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0744 AC: 5058 AN: 68020

Other (OTH) AF: 0.0595 AC: 125 AN: 2100

Alfa AF: 0.0679 Hom.: 599

Bravo AF: 0.0539

Asia WGS AF: 0.0850 AC: 295 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	11
DANN	Benign	0.40
PhyloP100		0.52

Splicing

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

Other links and lift over

dbSNP: rs17405722; hg19: chr17-40542501;