rs322185

chr17-27378727-C-T

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 0.643 in 151,980 control chromosomes in the GnomAD database, including 31,612 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 0.64 (31612 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.162

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.46).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.686 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: 0.643 AC: 97632 AN: 151862 Hom.: 31576 Cov.: 32

Gnomad AFR AF: 0.693

Gnomad AMI AF: 0.682

Gnomad AMR AF: 0.583

Gnomad ASJ AF: 0.652

Gnomad EAS AF: 0.692

Gnomad SAS AF: 0.552

Gnomad FIN AF: 0.674

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.623

Gnomad OTH AF: 0.645

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

GnomAD4 genome AF: 0.643 AC: 97731 AN: 151980 Hom.: 31612 Cov.: 32 AF XY: 0.643 AC XY: 47756 AN XY: 74280

Gnomad4 AFR AF: 0.693

Gnomad4 AMR AF: 0.583

Gnomad4 ASJ AF: 0.652

Gnomad4 EAS AF: 0.692

Gnomad4 SAS AF: 0.554

Gnomad4 FIN AF: 0.674

Gnomad4 NFE AF: 0.623

Gnomad4 OTH AF: 0.646

Alfa AF: 0.633 Hom.: 3800

Bravo AF: 0.639

Asia WGS AF: 0.616 AC: 2143 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.46
Cadd	Benign	6.9
Dann	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs322185; hg19: chr17-25705753;