17-56701456-A-T

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 0.306 in 152,068 control chromosomes in the GnomAD database, including 7,416 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 (7416 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.334 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: 0.307 AC: 46575 AN: 151950 Hom.: 7416 Cov.: 31

Gnomad AFR AF: 0.244

Gnomad AMI AF: 0.595

Gnomad AMR AF: 0.252

Gnomad ASJ AF: 0.263

Gnomad EAS AF: 0.280

Gnomad SAS AF: 0.305

Gnomad FIN AF: 0.442

Gnomad MID AF: 0.236

Gnomad NFE AF: 0.337

Gnomad OTH AF: 0.277

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

GnomAD4 genome AF: 0.306 AC: 46590 AN: 152068 Hom.: 7416 Cov.: 31 AF XY: 0.310 AC XY: 23031 AN XY: 74322

Gnomad4 AFR AF: 0.244

Gnomad4 AMR AF: 0.251

Gnomad4 ASJ AF: 0.263

Gnomad4 EAS AF: 0.281

Gnomad4 SAS AF: 0.304

Gnomad4 FIN AF: 0.442

Gnomad4 NFE AF: 0.337

Gnomad4 OTH AF: 0.277

Alfa AF: 0.322 Hom.: 4484

Bravo AF: 0.288

Asia WGS AF: 0.312 AC: 1083 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
Cadd	Benign	0.45
Dann	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs227724; hg19: chr17-54778817;