17-69924202-A-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 0.218 in 151,094 control chromosomes in the GnomAD database, including 4,561 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 0.22 (4561 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.40

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.509 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: 0.218 AC: 32890 AN: 150978 Hom.: 4567 Cov.: 30

Gnomad AFR AF: 0.0554

Gnomad AMI AF: 0.304

Gnomad AMR AF: 0.305

Gnomad ASJ AF: 0.273

Gnomad EAS AF: 0.525

Gnomad SAS AF: 0.263

Gnomad FIN AF: 0.307

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.252

Gnomad OTH AF: 0.265

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

GnomAD4 genome AF: 0.218 AC: 32885 AN: 151094 Hom.: 4561 Cov.: 30 AF XY: 0.224 AC XY: 16510 AN XY: 73778

Gnomad4 AFR AF: 0.0553

Gnomad4 AMR AF: 0.305

Gnomad4 ASJ AF: 0.273

Gnomad4 EAS AF: 0.526

Gnomad4 SAS AF: 0.263

Gnomad4 FIN AF: 0.307

Gnomad4 NFE AF: 0.252

Gnomad4 OTH AF: 0.267

Alfa AF: 0.224 Hom.: 464

Bravo AF: 0.218

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.28
Dann	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs180126; hg19: chr17-67920343; COSMIC: COSV64780794;