17-69954325-A-G

Variant names:

• chr17-69954325-A-G
• rs180084

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 0.716 in 152,048 control chromosomes in the GnomAD database, including 39,337 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 0.72 (39337 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.583

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 (EAS) allele frequency at 95% confidence interval = 0.937 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: 0.716 AC: 108715 AN: 151930 Hom.: 39280 Cov.: 32

Gnomad AFR AF: 0.785

Gnomad AMI AF: 0.775

Gnomad AMR AF: 0.725

Gnomad ASJ AF: 0.679

Gnomad EAS AF: 0.959

Gnomad SAS AF: 0.792

Gnomad FIN AF: 0.690

Gnomad MID AF: 0.753

Gnomad NFE AF: 0.652

Gnomad OTH AF: 0.698

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

GnomAD4 genome AF: 0.716 AC: 108832 AN: 152048 Hom.: 39337 Cov.: 32 AF XY: 0.720 AC XY: 53513 AN XY: 74328

Gnomad4 AFR AF: 0.786

Gnomad4 AMR AF: 0.725

Gnomad4 ASJ AF: 0.679

Gnomad4 EAS AF: 0.960

Gnomad4 SAS AF: 0.792

Gnomad4 FIN AF: 0.690

Gnomad4 NFE AF: 0.653

Gnomad4 OTH AF: 0.702

Alfa AF: 0.557 Hom.: 1457

Bravo AF: 0.724

Asia WGS AF: 0.875 AC: 3043 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	5.4
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs180084; hg19: chr17-67950466;