10-106552449-A-G

Variant names:

• chr10-106552449-A-G
• rs1341676

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 0.446 in 152,008 control chromosomes in the GnomAD database, including 17,023 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 (17023 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.84
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.681 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: 0.446 AC: 67754 AN: 151890 Hom.: 16977 Cov.: 32

Gnomad AFR AF: 0.687

Gnomad AMI AF: 0.356

Gnomad AMR AF: 0.350

Gnomad ASJ AF: 0.323

Gnomad EAS AF: 0.434

Gnomad SAS AF: 0.474

Gnomad FIN AF: 0.329

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.349

Gnomad OTH AF: 0.386

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

GnomAD4 genome AF: 0.446 AC: 67868 AN: 152008 Hom.: 17023 Cov.: 32 AF XY: 0.444 AC XY: 32963 AN XY: 74276

African (AFR) AF: 0.687 AC: 28491 AN: 41448

American (AMR) AF: 0.349 AC: 5331 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.323 AC: 1120 AN: 3468

East Asian (EAS) AF: 0.434 AC: 2234 AN: 5146

South Asian (SAS) AF: 0.473 AC: 2274 AN: 4804

European-Finnish (FIN) AF: 0.329 AC: 3485 AN: 10594

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.349 AC: 23708 AN: 67966

Other (OTH) AF: 0.388 AC: 818 AN: 2108

Alfa AF: 0.348 Hom.: 3233

Bravo AF: 0.452

Asia WGS AF: 0.480 AC: 1668 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.24
DANN	Benign	0.64
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs1341676; hg19: chr10-108312207;