17-69924202-A-T

Variant names:

• chr17-69924202-A-T
• rs180126

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;