rs6560787

chr10-2019767-G-Achr10-2019767-G-C

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 0.455 in 151,832 control chromosomes in the GnomAD database, including 15,984 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 0.45 (15984 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.111

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.679 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: 0.455 AC: 68957 AN: 151714 Hom.: 15964 Cov.: 31

Gnomad AFR AF: 0.406

Gnomad AMI AF: 0.282

Gnomad AMR AF: 0.424

Gnomad ASJ AF: 0.431

Gnomad EAS AF: 0.698

Gnomad SAS AF: 0.588

Gnomad FIN AF: 0.509

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.459

Gnomad OTH AF: 0.439

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

GnomAD4 genome AF: 0.455 AC: 69025 AN: 151832 Hom.: 15984 Cov.: 31 AF XY: 0.463 AC XY: 34337 AN XY: 74202

Gnomad4 AFR AF: 0.407

Gnomad4 AMR AF: 0.424

Gnomad4 ASJ AF: 0.431

Gnomad4 EAS AF: 0.698

Gnomad4 SAS AF: 0.588

Gnomad4 FIN AF: 0.509

Gnomad4 NFE AF: 0.458

Gnomad4 OTH AF: 0.443

Alfa AF: 0.461 Hom.: 7597

Bravo AF: 0.444

Asia WGS AF: 0.603 AC: 2100 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.0
Dann	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6560787; hg19: chr10-2061961;