rs17405722

Variant names:

• chr17-42390483-G-A
• rs17405722

Your query was ambiguous. Multiple possible variants found:

• chr17-42390483-G-A
• chr17-42390483-G-T

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 0.0611 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.0609 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

Gnomad4 AFR AF: 0.0377

Gnomad4 AMR AF: 0.0476

Gnomad4 ASJ AF: 0.0446

Gnomad4 EAS AF: 0.0178

Gnomad4 SAS AF: 0.0730

Gnomad4 FIN AF: 0.102

Gnomad4 NFE AF: 0.0744

Gnomad4 OTH AF: 0.0595

Alfa AF: 0.0694 Hom.: 491

Bravo AF: 0.0539

Asia WGS AF: 0.0850 AC: 295 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17405722; hg19: chr17-40542501;