17-34254988-G-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.343 in 151,906 control chromosomes in the GnomAD database, including 9,529 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 0.34 (9529 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.20

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.45).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.537 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: 0.343 AC: 52103 AN: 151788 Hom.: 9508 Cov.: 32

Gnomad AFR AF: 0.398

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.452

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.554

Gnomad SAS AF: 0.343

Gnomad FIN AF: 0.343

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.276

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.343 AC: 52170 AN: 151906 Hom.: 9529 Cov.: 32 AF XY: 0.350 AC XY: 25960 AN XY: 74218

Gnomad4 AFR AF: 0.398

Gnomad4 AMR AF: 0.453

Gnomad4 ASJ AF: 0.283

Gnomad4 EAS AF: 0.554

Gnomad4 SAS AF: 0.344

Gnomad4 FIN AF: 0.343

Gnomad4 NFE AF: 0.276

Gnomad4 OTH AF: 0.327

Alfa AF: 0.175 Hom.: 365

Bravo AF: 0.355

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.45
Cadd	Benign	15
Dann	Benign	0.88

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.080		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: rs2857656; hg19: chr17-32582007;