10-6000509-A-G

Position:

• chr10-6000509-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 0.0797 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;