rs17322780

Variant names:

• chr10-6000509-A-G
• rs17322780

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 0.0797 in 152,142 control chromosomes in the GnomAD database, including 526 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 0.080 (526 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0500

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0963 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0797 AC: 12119 AN: 152024 Hom.: 527 Cov.: 32

Gnomad AFR AF: 0.0634

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0643

Gnomad ASJ AF: 0.0528

Gnomad EAS AF: 0.0200

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.0859

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0974

Gnomad OTH AF: 0.0770

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

GnomAD4 genome AF: 0.0797 AC: 12133 AN: 152142 Hom.: 526 Cov.: 32 AF XY: 0.0789 AC XY: 5868 AN XY: 74374

Gnomad4 AFR AF: 0.0635

Gnomad4 AMR AF: 0.0642

Gnomad4 ASJ AF: 0.0528

Gnomad4 EAS AF: 0.0199

Gnomad4 SAS AF: 0.104

Gnomad4 FIN AF: 0.0859

Gnomad4 NFE AF: 0.0975

Gnomad4 OTH AF: 0.0767

Alfa AF: 0.0864 Hom.: 186

Bravo AF: 0.0757

Asia WGS AF: 0.0520 AC: 181 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.1
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17322780; hg19: chr10-6042472;