10-83396018-A-G

Variant names:

• chr10-83396018-A-G
• rs11592457

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 0.0658 in 149,868 control chromosomes in the GnomAD database, including 372 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 0.066 (372 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.548
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0933 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: 0.0657 AC: 9843 AN: 149750 Hom.: 367 Cov.: 31

Gnomad AFR AF: 0.0959

Gnomad AMI AF: 0.0747

Gnomad AMR AF: 0.0604

Gnomad ASJ AF: 0.0394

Gnomad EAS AF: 0.0476

Gnomad SAS AF: 0.0255

Gnomad FIN AF: 0.0870

Gnomad MID AF: 0.0510

Gnomad NFE AF: 0.0515

Gnomad OTH AF: 0.0484

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

GnomAD4 genome AF: 0.0658 AC: 9858 AN: 149868 Hom.: 372 Cov.: 31 AF XY: 0.0652 AC XY: 4767 AN XY: 73070

African (AFR) AF: 0.0958 AC: 3895 AN: 40664

American (AMR) AF: 0.0610 AC: 902 AN: 14794

Ashkenazi Jewish (ASJ) AF: 0.0394 AC: 136 AN: 3452

East Asian (EAS) AF: 0.0473 AC: 241 AN: 5092

South Asian (SAS) AF: 0.0253 AC: 118 AN: 4662

European-Finnish (FIN) AF: 0.0870 AC: 900 AN: 10340

Middle Eastern (MID) AF: 0.0548 AC: 16 AN: 292

European-Non Finnish (NFE) AF: 0.0515 AC: 3482 AN: 67596

Other (OTH) AF: 0.0484 AC: 100 AN: 2066

Alfa AF: 0.0615 Hom.: 81

Bravo AF: 0.0651

Asia WGS AF: 0.0370 AC: 127 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.6
DANN	Benign	0.60
PhyloP100		0.55

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs11592457; hg19: chr10-85155774;