chr10-2019767-G-A

Variant names:

• chr10-2019767-G-A
• rs6560787

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 0.455 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.407 AC: 16833 AN: 41378

American (AMR) AF: 0.424 AC: 6479 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.431 AC: 1495 AN: 3468

East Asian (EAS) AF: 0.698 AC: 3582 AN: 5130

South Asian (SAS) AF: 0.588 AC: 2823 AN: 4802

European-Finnish (FIN) AF: 0.509 AC: 5371 AN: 10542

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.458 AC: 31140 AN: 67922

Other (OTH) AF: 0.443 AC: 935 AN: 2110

Alfa AF: 0.460 Hom.: 8476

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
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs6560787; hg19: chr10-2061961;