17-5743244-A-G

Position:

• chr17-5743244-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 0.485 in 151,584 control chromosomes in the GnomAD database, including 18,031 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 0.49 (18031 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.108

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 (AMR) allele frequency at 95% confidence interval = 0.521 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: 0.485 AC: 73521 AN: 151464 Hom.: 18012 Cov.: 31

Gnomad AFR AF: 0.510

Gnomad AMI AF: 0.420

Gnomad AMR AF: 0.530

Gnomad ASJ AF: 0.569

Gnomad EAS AF: 0.278

Gnomad SAS AF: 0.440

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.436

Gnomad NFE AF: 0.482

Gnomad OTH AF: 0.498

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

GnomAD4 genome AF: 0.485 AC: 73591 AN: 151584 Hom.: 18031 Cov.: 31 AF XY: 0.483 AC XY: 35782 AN XY: 74036

Gnomad4 AFR AF: 0.510

Gnomad4 AMR AF: 0.530

Gnomad4 ASJ AF: 0.569

Gnomad4 EAS AF: 0.278

Gnomad4 SAS AF: 0.439

Gnomad4 FIN AF: 0.447

Gnomad4 NFE AF: 0.482

Gnomad4 OTH AF: 0.502

Alfa AF: 0.478 Hom.: 28678

Bravo AF: 0.490

Asia WGS AF: 0.385 AC: 1326 AN: 3450

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.9
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2215496; hg19: chr17-5646564;