chr17-53255898-G-A

Position:

• chr17-53255898-G-A

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 0.313 in 151,752 control chromosomes in the GnomAD database, including 8,698 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 0.31 (8698 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.208

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.729 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: 0.313 AC: 47488 AN: 151636 Hom.: 8690 Cov.: 31

Gnomad AFR AF: 0.164

Gnomad AMI AF: 0.430

Gnomad AMR AF: 0.422

Gnomad ASJ AF: 0.306

Gnomad EAS AF: 0.749

Gnomad SAS AF: 0.498

Gnomad FIN AF: 0.397

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.319

Gnomad OTH AF: 0.311

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

GnomAD4 genome AF: 0.313 AC: 47498 AN: 151752 Hom.: 8698 Cov.: 31 AF XY: 0.324 AC XY: 23998 AN XY: 74120

Gnomad4 AFR AF: 0.164

Gnomad4 AMR AF: 0.423

Gnomad4 ASJ AF: 0.306

Gnomad4 EAS AF: 0.748

Gnomad4 SAS AF: 0.496

Gnomad4 FIN AF: 0.397

Gnomad4 NFE AF: 0.319

Gnomad4 OTH AF: 0.319

Alfa AF: 0.326 Hom.: 3845

Bravo AF: 0.313

Asia WGS AF: 0.603 AC: 2094 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.1
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: rs1607979; hg19: chr17-51333259; COSMIC: COSV69487848;