17-27810524-A-G

Position:

• chr17-27810524-A-G

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 0.537 in 151,752 control chromosomes in the GnomAD database, including 23,900 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 0.54 (23900 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0610

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 = 0.724 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.537 AC: 81486 AN: 151634 Hom.: 23904 Cov.: 33

Gnomad AFR AF: 0.282

Gnomad AMI AF: 0.628

Gnomad AMR AF: 0.623

Gnomad ASJ AF: 0.587

Gnomad EAS AF: 0.744

Gnomad SAS AF: 0.696

Gnomad FIN AF: 0.630

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.628

Gnomad OTH AF: 0.567

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

GnomAD4 genome AF: 0.537 AC: 81497 AN: 151752 Hom.: 23900 Cov.: 33 AF XY: 0.542 AC XY: 40200 AN XY: 74120

Gnomad4 AFR AF: 0.282

Gnomad4 AMR AF: 0.623

Gnomad4 ASJ AF: 0.587

Gnomad4 EAS AF: 0.744

Gnomad4 SAS AF: 0.695

Gnomad4 FIN AF: 0.630

Gnomad4 NFE AF: 0.628

Gnomad4 OTH AF: 0.566

Alfa AF: 0.564 Hom.: 3068

Bravo AF: 0.527

Asia WGS AF: 0.677 AC: 2355 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.8
DANN	Benign	0.55

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs2531863; hg19: chr17-26137550;