10-100615605-A-G

Variant names:

• chr10-100615605-A-G
• rs2489029

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 0.47 in 152,042 control chromosomes in the GnomAD database, including 17,662 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 0.47 (17662 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0140
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.556 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.470 AC: 71461 AN: 151922 Hom.: 17652 Cov.: 32

Gnomad AFR AF: 0.333

Gnomad AMI AF: 0.626

Gnomad AMR AF: 0.467

Gnomad ASJ AF: 0.608

Gnomad EAS AF: 0.289

Gnomad SAS AF: 0.405

Gnomad FIN AF: 0.479

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.561

Gnomad OTH AF: 0.511

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

GnomAD4 genome AF: 0.470 AC: 71503 AN: 152042 Hom.: 17662 Cov.: 32 AF XY: 0.464 AC XY: 34509 AN XY: 74330

African (AFR) AF: 0.333 AC: 13828 AN: 41464

American (AMR) AF: 0.467 AC: 7141 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.608 AC: 2111 AN: 3472

East Asian (EAS) AF: 0.288 AC: 1484 AN: 5148

South Asian (SAS) AF: 0.406 AC: 1959 AN: 4820

European-Finnish (FIN) AF: 0.479 AC: 5070 AN: 10590

Middle Eastern (MID) AF: 0.531 AC: 156 AN: 294

European-Non Finnish (NFE) AF: 0.561 AC: 38111 AN: 67940

Other (OTH) AF: 0.509 AC: 1073 AN: 2110

Alfa AF: 0.508 Hom.: 28789

Bravo AF: 0.468

Asia WGS AF: 0.353 AC: 1227 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.1
DANN	Benign	0.37
PhyloP100		-0.014

Splicing

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

Other links and lift over

dbSNP: rs2489029; hg19: chr10-102375362;