17-69925616-T-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 0.668 in 139,754 control chromosomes in the GnomAD database, including 31,546 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 0.67 (31546 hom., cov: 21)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.35

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.936 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.668 AC: 93333 AN: 139644 Hom.: 31514 Cov.: 21

Gnomad AFR AF: 0.644

Gnomad AMI AF: 0.772

Gnomad AMR AF: 0.700

Gnomad ASJ AF: 0.685

Gnomad EAS AF: 0.959

Gnomad SAS AF: 0.771

Gnomad FIN AF: 0.660

Gnomad MID AF: 0.765

Gnomad NFE AF: 0.647

Gnomad OTH AF: 0.659

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

GnomAD4 genome AF: 0.668 AC: 93410 AN: 139754 Hom.: 31546 Cov.: 21 AF XY: 0.672 AC XY: 45235 AN XY: 67352

Gnomad4 AFR AF: 0.644

Gnomad4 AMR AF: 0.700

Gnomad4 ASJ AF: 0.685

Gnomad4 EAS AF: 0.959

Gnomad4 SAS AF: 0.772

Gnomad4 FIN AF: 0.660

Gnomad4 NFE AF: 0.647

Gnomad4 OTH AF: 0.663

Alfa AF: 0.657 Hom.: 3547

Bravo AF: 0.684

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.76
Dann	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs180120; hg19: chr17-67921757;