rs17322780

Variant names:

• chr10-6000509-A-G
• rs17322780

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0635 AC: 2635 AN: 41520

American (AMR) AF: 0.0642 AC: 981 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0528 AC: 183 AN: 3468

East Asian (EAS) AF: 0.0199 AC: 103 AN: 5176

South Asian (SAS) AF: 0.104 AC: 499 AN: 4808

European-Finnish (FIN) AF: 0.0859 AC: 910 AN: 10588

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.0975 AC: 6625 AN: 67972

Other (OTH) AF: 0.0767 AC: 162 AN: 2112

Alfa AF: 0.0860 Hom.: 1166

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
PhyloP100		-0.050

Splicing

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

Other links and lift over

dbSNP: rs17322780; hg19: chr10-6042472;