17-39950346-A-G

Position:

• chr17-39950346-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 0.593 in 151,736 control chromosomes in the GnomAD database, including 27,215 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 0.59 (27215 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.597

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.688 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: 0.593 AC: 89885 AN: 151618 Hom.: 27188 Cov.: 30

Gnomad AFR AF: 0.695

Gnomad AMI AF: 0.591

Gnomad AMR AF: 0.637

Gnomad ASJ AF: 0.542

Gnomad EAS AF: 0.692

Gnomad SAS AF: 0.623

Gnomad FIN AF: 0.534

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.524

Gnomad OTH AF: 0.564

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

GnomAD4 genome AF: 0.593 AC: 89957 AN: 151736 Hom.: 27215 Cov.: 30 AF XY: 0.595 AC XY: 44089 AN XY: 74096

Gnomad4 AFR AF: 0.695

Gnomad4 AMR AF: 0.637

Gnomad4 ASJ AF: 0.542

Gnomad4 EAS AF: 0.691

Gnomad4 SAS AF: 0.622

Gnomad4 FIN AF: 0.534

Gnomad4 NFE AF: 0.524

Gnomad4 OTH AF: 0.565

Alfa AF: 0.558 Hom.: 5901

Bravo AF: 0.610

Asia WGS AF: 0.624 AC: 2169 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8071050; hg19: chr17-38106599;