17-61420889-A-G

Position:

• chr17-61420889-A-G

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 0.708 in 152,008 control chromosomes in the GnomAD database, including 38,396 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 0.71 (38396 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.47

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.788 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.707 AC: 107435 AN: 151888 Hom.: 38347 Cov.: 31

Gnomad AFR AF: 0.795

Gnomad AMI AF: 0.662

Gnomad AMR AF: 0.662

Gnomad ASJ AF: 0.704

Gnomad EAS AF: 0.693

Gnomad SAS AF: 0.626

Gnomad FIN AF: 0.737

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.668

Gnomad OTH AF: 0.679

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

GnomAD4 genome AF: 0.708 AC: 107546 AN: 152008 Hom.: 38396 Cov.: 31 AF XY: 0.710 AC XY: 52736 AN XY: 74276

Gnomad4 AFR AF: 0.796

Gnomad4 AMR AF: 0.663

Gnomad4 ASJ AF: 0.704

Gnomad4 EAS AF: 0.694

Gnomad4 SAS AF: 0.625

Gnomad4 FIN AF: 0.737

Gnomad4 NFE AF: 0.668

Gnomad4 OTH AF: 0.678

Alfa AF: 0.689 Hom.: 5860

Bravo AF: 0.707

Asia WGS AF: 0.658 AC: 2291 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.020
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: rs9905385; hg19: chr17-59498250;