17-392044-T-G

Variant names:

• chr17-392044-T-G
• rs8077538

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.857 in 152,176 control chromosomes in the GnomAD database, including 56,518 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 0.86 (56518 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.176
• Publications: 18 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.857 AC: 130383 AN: 152058 Hom.: 56497 Cov.: 32

Gnomad AFR AF: 0.721

Gnomad AMI AF: 0.787

Gnomad AMR AF: 0.912

Gnomad ASJ AF: 0.882

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.964

Gnomad FIN AF: 0.878

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.906

Gnomad OTH AF: 0.868

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

GnomAD4 genome AF: 0.857 AC: 130457 AN: 152176 Hom.: 56518 Cov.: 32 AF XY: 0.860 AC XY: 64023 AN XY: 74412

African (AFR) AF: 0.720 AC: 29881 AN: 41474

American (AMR) AF: 0.912 AC: 13937 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.882 AC: 3061 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5173 AN: 5176

South Asian (SAS) AF: 0.965 AC: 4663 AN: 4834

European-Finnish (FIN) AF: 0.878 AC: 9299 AN: 10596

Middle Eastern (MID) AF: 0.847 AC: 249 AN: 294

European-Non Finnish (NFE) AF: 0.906 AC: 61641 AN: 68018

Other (OTH) AF: 0.869 AC: 1837 AN: 2114

Alfa AF: 0.880 Hom.: 94503

Bravo AF: 0.852

Asia WGS AF: 0.966 AC: 3359 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.2
DANN	Benign	0.68
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs8077538; hg19: chr17-241835;